CHARMM: the biomolecular simulation program (Q24658108)

22 June 2017

title

CHARMM: the biomolecular simulation program (English)

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computational mathematics

22 June 2017

main subject

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35

M Karplus

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C Bartels

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Stefan Boresch

object named as

S Boresch

10

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Lennart Nilsson

object named as

L Nilsson

4

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Emanuele Paci

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object named as

E Paci

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B R Brooks

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C L Brooks

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A D Mackerell

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R J Petrella

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B Roux

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G Archontis

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A Caflisch

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L Caves

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Q Cui

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A R Dinner

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M Feig

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S Fischer

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J Gao

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M Hodoscek

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K Kuczera

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T Lazaridis

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V Ovchinnikov

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R W Pastor

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C B Post

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M Schaefer

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H L Woodcock

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W Yang

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D M York

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Y Won

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W Im

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J Ma

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J Z Pu

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B Tidor

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R M Venable

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X Wu

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22 June 2017

publication date

1 July 2009

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Journal of Computational Chemistry

22 June 2017

language of work or name

English

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published in

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22 June 2017

volume

30

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22 June 2017

issue

10

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22 June 2017

page(s)

1545-1614

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publication type of scholarly work

22 June 2017

review article

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Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy

7 April 2017

1 reference

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Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations.

7 April 2017

1 reference

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An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

7 April 2017

1 reference

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Domain movements in human fatty acid synthase by quantized elastic deformational model

7 April 2017

1 reference

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Atomic solvation parameters applied to molecular dynamics of proteins in solution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Cell biology: Ripping up the nuclear envelope

7 April 2017

1 reference

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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

7 April 2017

1 reference

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Multicanonical ensemble: A new approach to simulate first-order phase transitions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Mutagenesis and modeling of the peroxiredoxin (Prx) complex with the NMR structure of ATP-bound human sulfiredoxin implicate aspartate 187 of Prx I as the catalytic residue in ATP hydrolysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The structural basis for the transition from Ras-GTP to Ras-GDP

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Control of the selectivity of the aquaporin water channel family by global orientational tuning

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Crystallographic R factor refinement by molecular dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

GROMACS: fast, flexible, and free

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The Amber biomolecular simulation programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

VMD: visual molecular dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The interpretation of protein structures: Estimation of static accessibility

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics and protein function

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How enzymes work: analysis by modern rate theory and computer simulations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Evaluation of a fast implicit solvent model for molecular dynamics simulations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Uracil-DNA glycosylase acts by substrate autocatalysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Triosephosphate isomerase: a theoretical comparison of alternative pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Protein folding and function: the N-terminal fragment in adenylate kinase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A dynamic model for the allosteric mechanism of GroEL

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Discrimination of the native from misfolded protein models with an energy function including implicit solvation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Effective energy function for proteins in solution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Solvation energy in protein folding and binding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamics of folded proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Canonical dynamics: Equilibrium phase-space distributions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Discovering high-affinity ligands for proteins: SAR by NMR

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Essential dynamics of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structural Determinants of Transmembrane β-Barrels

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

CHARMMing: a new, flexible web portal for CHARMM.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The human cytomegalovirus UL44 C clamp wraps around DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Single-molecule approach to molecular biology in living bacterial cells

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Additive empirical force field for hexopyranose monosaccharides

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Understanding the dielectric properties of liquid amides from a polarizable force field.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Finding transition pathways using the string method with swarms of trajectories

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Reaction coordinate of an enzymatic reaction revealed by transition path sampling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Modeling the kinetics of bimolecular reactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Conformational sampling with implicit solvent models: application to the PHF6 peptide in tau protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Advances in methods and algorithms in a modern quantum chemistry program package.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Mechanisms and free energies of enzymatic reactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Neutralization epitope responsible for the hepatitis B virus subtype-specific protection in chimpanzees

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The midpoint method for parallelization of particle simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Recent advances in molecular simulations of ion solvation at liquid interfaces

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Specific ion effects at the air/water interface

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The GROMOS software for biomolecular simulation: GROMOS05.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular origin of time-dependent fluorescence shifts in proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Comparison of mode analyses at different resolutions applied to nucleic acid systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Calculation of absolute protein-ligand binding free energy from computer simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structural mechanism of the recovery stroke in the myosin molecular motor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Constant pH molecular dynamics with proton tautomerism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Phi-value analysis by molecular dynamics simulations of reversible folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Hidden complexity of free energy surfaces for peptide (protein) folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Exploring peptide energy landscapes: a test of force fields and implicit solvent models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Calculating potentials of mean force from steered molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The unfolding action of GroEL on a protein substrate

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Recent advances in the development and application of implicit solvent models in biomolecule simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Energetics of ion conduction through the gramicidin channel

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Fast protein folding on downhill energy landscape

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How dihydrofolate reductase facilitates protonation of dihydrofolate

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Analysis of the distributed computing approach applied to the folding of a small beta peptide

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

DNA polymorphism: a comparison of force fields for nucleic acids

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The missing link between thermodynamics and structure in F1-ATPase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Determination of a transition state at atomic resolution from protein engineering data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The origins of asymmetry in the folding transition states of protein L and protein G.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Translocation mechanism of long sugar chains across the maltoporin membrane channel

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Evaluating CASP4 predictions with physical energy functions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulations of biomolecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How to describe protein motion without amino acid sequence and atomic coordinates

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Protein and peptide folding explored with molecular simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Lipid bilayers, NMR relaxation, and computer simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free energy simulations come of age: protein-ligand recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Evolution and physics in comparative protein structure modeling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulations of protein folding from the transition state

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Quantum mechanical methods for enzyme kinetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Theoretical and computational models of ion channels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Development and current status of the CHARMM force field for nucleic acids.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Use of MCSS to design small targeted libraries: application to picornavirus ligands.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Extending the accuracy limits of prediction for side-chain conformations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free energy decomposition of protein-protein interactions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Solvent effects on the energy landscapes and folding kinetics of polyalanine

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Anisotropy of fluctuation dynamics of proteins with an elastic network model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulations of human rhinovirus and an antiviral compound

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics of the anticodon domain of yeast tRNA(Phe): codon-anticodon interaction.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Generalized born models of macromolecular solvation effects

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Folding simulations of a three-stranded antiparallel beta -sheet peptide

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

On the truncation of long-range electrostatic interactions in DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: a simulation study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Unfolding proteins by external forces and temperature: the importance of topology and energetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Understanding beta-hairpin formation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Biomolecular electrostatics with the linearized Poisson-Boltzmann equation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular Dynamics Simulation of Melittin in a Dimyristoylphosphatidylcholine Bilayer Membrane

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The allosteric mechanism of the chaperonin GroEL: A dynamic analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular picture of folding of a small α/β protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Energetics of Quasiequivalence: Computational Analysis of Protein-Protein Interactions in Icosahedral Viruses

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Reconstructing potential energy functions from simulated force-induced unbinding processes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Thermodynamics and kinetics of a Brownian motor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The statistical-thermodynamic basis for computation of binding affinities: a critical review

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics study of unbinding of the avidin-biotin complex

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Solving the structures of macromolecular complexes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Simulation methods for protein structure fluctuations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamical theory of activated processes in globular proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Active site dynamics of ribonuclease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free energy via molecular simulation: applications to chemical and biomolecular systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Mechanism of tertiary structural change in hemoglobin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

On using time-averaging restraints in molecular dynamics simulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

New algorithms and an in silico benchmark for computational enzyme design

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Influence of the membrane potential on the free energy of an intrinsic protein

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

"New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The effects of truncating long-range forces on protein dynamics

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Simulation analysis of the stability mutant R96H of T4 lysozyme

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A molecular dynamics study of conformational changes and hydration of left-handed d(CGCGCGCGCGCG)2 in a nonsalt solution

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The implementation of a fast and accurate QM/MM potential method in Amber

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Implicit nonpolar solvent models

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

FACTS: Fast analytical continuum treatment of solvation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Explanation of the Unusual Temperature Dependence of the Atmospherically Important OH + H2S → H2O + HS Reaction and Prediction of the Rate Constant at Combustion Temperatures

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Protein-protein docking with backbone flexibility

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

FireDock: fast interaction refinement in molecular docking

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Automatic method for identifying reaction coordinates in complex systems

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Finite temperature string method for the study of rare events

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

String method in collective variables: minimum free energy paths and isocommittor surfaces

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Simulation studies of the protein-water interface. I. Properties at the molecular resolution

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Dynamic coupling between coordinates in a model for biomolecular isomerization

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Optimal estimates of free energies from multistate nonequilibrium work data

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure of a transient intermediate for GTP hydrolysis by ras.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Calculations of pH-dependent binding of proteins to biological membranes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A molecular dynamics approach to the structural characterization of amyloid aggregation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Monte Carlo simulations of biomolecules: The MC module in CHARMM.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Structure-based design of novel Chk1 inhibitors: insights into hydrogen bonding and protein-ligand affinity

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Alchemical free energy calculations and multiple conformational substates

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Thermal unfolding simulations of a multimeric protein-Transition state and unfolding pathways

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

The contribution of C alpha-H...O hydrogen bonds to membrane protein stability depends on the position of the amide

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Implicit solvent simulations of peptide interactions with anionic lipid membranes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Refinement of NMR structures using implicit solvent and advanced sampling techniques

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Constant pH molecular dynamics in generalized Born implicit solvent

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Grand canonical Monte Carlo simulations of water in protein environments

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular simulation of the reversible mechanical unfolding of proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Assessing scoring functions for protein-ligand interactions

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2810661

Improved treatment of the protein backbone in empirical force fields.

28 November 2018

1 reference

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Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

28 November 2018

1 reference

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Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase

28 November 2018

1 reference

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Balancing Kinetic and Thermodynamic Control: the Mechanism of Carbocation Cyclization by Squalene Cyclase

28 November 2018

1 reference

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Generalized born model with a simple smoothing function

28 November 2018

1 reference

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Effective energy function for proteins in lipid membranes

28 November 2018

1 reference

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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

28 November 2018

1 reference

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Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase

28 November 2018

1 reference

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An improved method for nonbonded list generation: rapid determination of near-neighbor pairs

28 November 2018

1 reference

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Structure activity relationship by NMR and by computer: a comparative study

28 November 2018

1 reference

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Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

28 November 2018

1 reference

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Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

28 November 2018

1 reference

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Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

28 November 2018

1 reference

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Modern protein force fields behave comparably in molecular dynamics simulations

28 November 2018

1 reference

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Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

28 November 2018

1 reference

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Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

28 November 2018

1 reference

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Combined QM/MM study of the opsin shift in bacteriorhodopsin

28 November 2018

1 reference

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Identifying native-like protein structures using physics-based potentials

28 November 2018

1 reference

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Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

28 November 2018

1 reference

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Energetics of ion conduction through the K+ channel

28 November 2018

1 reference

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The energetics of off-rotamer protein side-chain conformations

28 November 2018

1 reference

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Protein molecular dynamics with the generalized born/ACE solvent model

28 November 2018

1 reference

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Rigorous classical-mechanical derivation of a multiple-copy algorithm for sampling statistical mechanical ensembles

28 November 2018

1 reference

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Building-block approach for determining low-frequency normal modes of macromolecules

28 November 2018

1 reference

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MCSS functionality maps for a flexible protein

28 November 2018

1 reference

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Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

28 November 2018

1 reference

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Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide

28 November 2018

1 reference

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Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure

28 November 2018

1 reference

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Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

28 November 2018

1 reference

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Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

28 November 2018

1 reference

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Conformational transitions using molecular dynamics with minimum biasing.

28 November 2018

1 reference

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A structure refinement method based on molecular dynamics in four spatial dimensions

28 November 2018

1 reference

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The contribution of vibrational entropy to molecular association. The dimerization of insulin.

28 November 2018

1 reference

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Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin

28 November 2018

1 reference

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A molecular dynamics study of gating in dioxolane-linked gramicidin A channels

28 November 2018

1 reference

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Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

28 November 2018

1 reference

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Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

28 November 2018

1 reference

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Functionality maps of binding sites: a multiple copy simultaneous search method

28 November 2018

1 reference

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Hybrid Monte Carlo method for condensed-matter systems

28 November 2018

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12 December 2020

Optimized Monte Carlo data analysis

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12 December 2020

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

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12 December 2020

Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes

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12 December 2020

Solvent mobility and the protein 'glass' transition

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12 December 2020

Computer simulations of protein folding by targeted molecular dynamics

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12 December 2020

On the unfolding of alpha-lytic protease and the role of the pro region

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12 December 2020

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

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12 December 2020

Molecular dynamics simulations of biomolecules

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12 December 2020

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

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12 December 2020

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase

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12 December 2020

Association of protein-DNA recognition complexes: electrostatic and nonelectrostatic effects

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12 December 2020

Potentials of mean force between ionizable amino acid side chains in water

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12 December 2020

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

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12 December 2020

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12 December 2020

Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail

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12 December 2020

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12 December 2020

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

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12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

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12 December 2020

Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes

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12 December 2020

Isotropic periodic sum: a method for the calculation of long-range interactions

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12 December 2020

Protein structural change upon ligand binding: linear response theory

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12 December 2020

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

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12 December 2020

Absolute free energy calculations by thermodynamic integration in four spatial dimensions

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12 December 2020

A skewed-momenta method to efficiently generate conformational-transition trajectories

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12 December 2020

Energetics of the native and non-native states of the glycophorin transmembrane helix dimer

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12 December 2020

Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field

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12 December 2020

Voltage-dependent energetics of alamethicin monomers in the membrane

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12 December 2020

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12 December 2020

Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field

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12 December 2020

Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field based on Drude oscillators

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12 December 2020

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

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12 December 2020

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

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12 December 2020

Bias annealing: a method for obtaining transition paths de novo

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12 December 2020

Heat capacity and compactness of denatured proteins

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12 December 2020

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

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12 December 2020

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method

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12 December 2020

Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms

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12 December 2020

Aberrant agouti-related protein system in the hypothalamus of the anx/anx mouse is associated with activation of microglia

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12 December 2020

CHARMM-GUI: a web-based graphical user interface for CHARMM

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12 December 2020

Importance of van der Waals Interactions in QM/MM Simulations

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12 December 2020

Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

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12 December 2020

Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives

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12 December 2020

Thermodynamics of amide hydrogen bond formation in polar and apolar solvents

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12 December 2020

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

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12 December 2020

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

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12 December 2020

Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials.

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12 December 2020

Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins

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12 December 2020

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant

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12 December 2020

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12 December 2020

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

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12 December 2020

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

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12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

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12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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12 December 2020

Quantum simulation of ferrocytochrome c

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12 December 2020

Free energy simulations

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12 December 2020

A mathematical model for structure-function relations in hemoglobin

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12 December 2020

Dynamics of ligand binding to heme proteins

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12 December 2020

Refinement of protein conformations using a macromolecular energy minimization procedure

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12 December 2020

Molecular dynamics of native protein. II. Analysis and nature of motion

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12 December 2020

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

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12 December 2020

Affinities of amino acid side chains for solvent water

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12 December 2020

Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies

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12 December 2020

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP)

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12 December 2020

First-principles calculation of the folding free energy of a three-helix bundle protein

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12 December 2020

Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-O

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12 December 2020

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase

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12 December 2020

Hydrophilicity of cavities in proteins

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12 December 2020

Calculations on folding of segment B1 of streptococcal protein G 1 1Edited by F. Cohen

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12 December 2020

Protein sidechain conformer prediction: a test of the energy function

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12 December 2020

Energy landscape of a native protein: jumping-among-minima model

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12 December 2020

Efficient Monte Carlo methods for the computer simulation of biological molecules

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12 December 2020

Q-Chem 2.0: a high-performanceab initio electronic structure program package

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Die Berechnung optischer und elektrostatischer Gitterpotentiale

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7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

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7 January 2021

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

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7 January 2021

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

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7 January 2021

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7 January 2021

Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

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7 January 2021

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7 January 2021

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

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7 January 2021

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7 January 2021

Symplectic Numerical Integrators in Constrained Hamiltonian Systems

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution

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7 January 2021

GROMACS 3.0: a package for molecular simulation and trajectory analysis

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7 January 2021

Pairwise solute descreening of solute charges from a dielectric medium

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7 January 2021

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

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7 January 2021

A fast algorithm for particle simulations

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7 January 2021

A polarizable model of water for molecular dynamics simulations of biomolecules

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7 January 2021

Analyzing biased Monte Carlo and molecular dynamics simulations

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7 January 2021

Replica-exchange molecular dynamics method for protein folding

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7 January 2021

High performance computational chemistry: An overview of NWChem a distributed parallel application

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7 January 2021

Direct Observation of the Transition State

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7 January 2021

Theoretical studies of van der Waals molecules and intermolecular forces

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7 January 2021

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7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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7 January 2021

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7 January 2021

Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain−Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations

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7 January 2021

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

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7 January 2021

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

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7 January 2021

Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

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7 January 2021

Creating a regular array of metal-complexing molecules on an insulator surface at room temperature

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7 January 2021

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7 January 2021

Electrostatic free energy calculations using the generalized solvent boundary potential method

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7 January 2021

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

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7 January 2021

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

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7 January 2021

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7 January 2021

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7 January 2021

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

Stochastic Problems in Physics and Astronomy

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Climatic impact of tropical lowland deforestation on nearby montane cloud forests

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7 January 2021

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21287

A Smooth Solvation Potential Based on the Conductor-Like Screening Model

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21287

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21287

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11 October 2022

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11 October 2022

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COCI

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22 October 2022

Identifiers

DOI

10.1002/JCC.21287

1 reference

journals/jcc/BrooksBMNPRWABBCCCDFFGHIKLMOPPPPSTVWWYYK09

22 June 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

OpenCitations bibliographic resource ID

28 January 2021

151602

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

151602

1 reference