Fast geometric consensus approach for protein model quality assessment (Q30398676)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

title

Fast geometric consensus approach for protein model quality assessment (English)

1 reference

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20 January 2020

4

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20 January 2020

author name string

Rafal Adamczak

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

Jaroslaw Pillardy

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

Brinda K Vallat

series ordinal

3

1 reference

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20 January 2020

publication date

18 January 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computational Biology

20 January 2020

language of work or name

English

0 references

published in

1 reference

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20 January 2020

volume

18

1 reference

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20 January 2020

issue

12

1 reference

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20 January 2020

page(s)

1807-1818

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Atomically detailed simulation of the recovery stroke in myosin by Milestoning

20 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Evaluation of CASP8 model quality predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Building and assessing atomic models of proteins from structural templates: learning and benchmarks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Information theory provides a comprehensive framework for the evaluation of protein structure predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Progress and challenges in protein structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Ranking predicted protein structures with support vector regression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

QMEAN: A comprehensive scoring function for model quality assessment.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Critical assessment of methods of protein structure prediction-Round VII

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Benchmarking consensus model quality assessment for protein fold recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Evaluation of 3D-Jury on CASP7 models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Analysis of TASSER-based CASP7 protein structure prediction results

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Ab initio modeling of small proteins by iterative TASSER simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

A composite score for predicting errors in protein structure models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Critical assessment of methods of protein structure prediction (CASP)--round 6.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Scoring function for automated assessment of protein structure template quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Accurate prediction of solvent accessibility using neural networks-based regression.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Local feature frequency profile: a method to measure structural similarity in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

LGA: A method for finding 3D similarities in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

3D-Jury: a simple approach to improve protein structure predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Pcons: a neural-network-based consensus predictor that improves fold recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

A study of quality measures for protein threading models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

A distance-dependent atomic knowledge-based potential for improved protein structure selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

MaxSub: an automated measure for the assessment of protein structure prediction quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Discrimination of near-native protein structures from misfolded models by empirical free energy functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Ab initio construction of protein tertiary structures using a hierarchical approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Processing and analysis of CASP3 protein structure predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction 1 1Edited by F. Cohen

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Assessment of protein models with three-dimensional profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Critical assessment of methods of protein structure prediction - Round VIII.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Assessment of global and local model quality in CASP8 using Pcons and ProQ

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

The ModFOLD server for the quality assessment of protein structural models

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Foldamer dynamics expressed via Markov state models. II. State space decomposition

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

SPARKS 2 and SP3 servers in CASP6.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Improving sequence-based fold recognition by using 3D model quality assessment

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Hamming distance geometry of a protein conformational space: application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3228594

Linear programming optimization and a double statistical filter for protein threading protocols

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21244273

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21244273

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1089/CMB.2010.0170

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

journals/jcb/AdamczakPVM11

20 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21244273%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

PubMed publication ID

21244273

1 reference