AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening (Q93143015)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

title

AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

1 reference

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

author name string

Duc Duy Nguyen

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

publication date

1 July 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Information and Modeling

3 May 2020

language of work or name

English

0 references

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

volume

59

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

page(s)

3291-3304

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

DG-GL: Differential geometry-based geometric learning of molecular datasets.

3 May 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Comparative Assessment of Scoring Functions: The CASF-2016 Update

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Development and evaluation of a deep learning model for protein-ligand binding affinity prediction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

MoleculeNet: a benchmark for molecular machine learning.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

KDEEP: Protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Rigidity Strengthening: A Mechanism for Protein-Ligand Binding.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Predicting protein-ligand affinity with a random matrix framework

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Generalized flexibility-rigidity index.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

STRUM: structure-based prediction of protein stability changes upon single-point mutation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Low-Quality Structural and Interaction Data Improves Binding Affinity Prediction via Random Forest.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Communication: Capturing protein multiscale thermal fluctuations.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Protein contact network topology: a natural language for allostery.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Classification of Current Scoring Functions

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Beware of machine learning-based scoring functions-on the danger of developing black boxes

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

ChemNetworks: A complex network analysis tool for chemical systems

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

mCSM: predicting the effects of mutations in proteins using graph-based signatures.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Ligand Identification Scoring Algorithm (LISA).

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A machine learning-based method to improve docking scoring functions and its application to drug repurposing

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Comparative assessment of scoring functions on a diverse test set.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A graph-theory algorithm for rapid protein side-chain prediction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Tailoring wavelets for chaos control

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Protein flexibility predictions using graph theory

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Conformational change of proteins arising from normal mode calculations

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Anisotropy of fluctuation dynamics of proteins with an elastic network model

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A general and fast scoring function for protein-ligand interactions: a simplified potential approach

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Analysis of domain motions by approximate normal mode calculations

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

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

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Development and validation of a genetic algorithm for flexible docking

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

A fast flexible docking method using an incremental construction algorithm.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Normal vibrations of proteins: glucagon

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Dynamics of a small globular protein in terms of low-frequency vibrational modes

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6664294

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

11 February 2021

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Topological Index. A Newly Proposed Quantity Characterizing the Topological Nature of Structural Isomers of Saturated Hydrocarbons

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Statistical Thermodynamics of Random Networks [and Discussion]

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Networks: An introduction

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Topological Persistence and Simplification

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Computing Persistent Homology

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

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

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00334

Identifiers

DOI

10.1021/ACS.JCIM.9B00334

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31257871%20AND%20SRC:MED&resulttype=core&format=json

3 May 2020

PubMed publication ID

31257871

1 reference