(Q38305525)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11131967%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

title

Deciphering common failures in molecular docking of ligand-protein complexes (English)

1 reference

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3 November 2019

1 reference

11

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3 November 2019

Gennady Verkhivker

1

1 reference

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3 November 2019

author name string

D Bouzida

2

1 reference

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3 November 2019

D K Gehlhaar

3

1 reference

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3 November 2019

P A Rejto

4

1 reference

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3 November 2019

S Arthurs

5

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3 November 2019

A B Colson

6

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3 November 2019

S T Freer

7

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3 November 2019

V Larson

8

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3 November 2019

B A Luty

9

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3 November 2019

T Marrone

10

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3 November 2019

publication date

1 November 2000

1 reference

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Journal of Computer - Aided Molecular Design

3 November 2019

published in

1 reference

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3 November 2019

volume

14

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3 November 2019

issue

8

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3 November 2019

page(s)

731-751

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Flexible ligand docking using a genetic algorithm.

3 November 2019

cites work

1 reference

12 December 2020

Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin

1 reference

12 December 2020

New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking

1 reference

12 December 2020

Protein folding via binding and vice versa

1 reference

12 December 2020

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

1 reference

12 December 2020

A comparison of heuristic search algorithms for molecular docking.

1 reference

12 December 2020

Structure-based strategies for drug design and discovery

1 reference

12 December 2020

Quantifying biological specificity: the statistical mechanics of molecular recognition

1 reference

12 December 2020

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

1 reference

12 December 2020

Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy

1 reference

12 December 2020

Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form

1 reference

12 December 2020

Characterization of receptors with a new negative image: use in molecular docking and lead optimization

1 reference

12 December 2020

Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

1 reference

12 December 2020

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding

1 reference

12 December 2020

Monte Carlo docking of oligopeptides to proteins.

1 reference

12 December 2020

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

1 reference

12 December 2020

Ligand docking to proteins with discrete side-chain flexibility.

1 reference

12 December 2020

Protein conformational substates from X-ray crystallography

1 reference

12 December 2020

Development and validation of a genetic algorithm for flexible docking

1 reference

12 December 2020

Flexible ligand docking using conformational ensembles

1 reference

12 December 2020

Modelling protein docking using shape complementarity, electrostatics and biochemical information

1 reference

12 December 2020

Protein docking and complementarity

1 reference

12 December 2020

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions

1 reference

12 December 2020

Accommodating protein flexibility in computational drug design

1 reference

12 December 2020

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

1 reference

12 December 2020

Flexible Docking and Design

1 reference

12 December 2020

A continuum model for protein-protein interactions: application to the docking problem.

1 reference

12 December 2020

Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively

1 reference

12 December 2020

CombiDOCK: structure-based combinatorial docking and library design

1 reference

12 December 2020

Clustering of low-energy conformations near the native structures of small proteins

1 reference

12 December 2020

Fitting an inhibitor into the active site of thermolysin: a molecular dynamics case study

1 reference

12 December 2020

Theoretical studies of protein-folding thermodynamics and kinetics

1 reference

12 December 2020

Flexible protein-ligand docking by global energy optimization in internal coordinates.

1 reference

12 December 2020

From Levinthal to pathways to funnels

1 reference

12 December 2020

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

1 reference

12 December 2020

Folding funnels, binding funnels, and protein function

1 reference

12 December 2020

Principles of protein folding--a perspective from simple exact models.

1 reference

12 December 2020

Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.

1 reference

12 December 2020

The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution

1 reference

12 December 2020

Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes

1 reference

12 December 2020

Docking small-molecule ligands into active sites

1 reference

12 December 2020

Efficient Monte Carlo methods for the computer simulation of biological molecules

1 reference

12 December 2020

Ligand solvation in molecular docking.

1 reference

12 December 2020

Funnels, pathways, and the energy landscape of protein folding: a synthesis

1 reference

12 December 2020

Flexible docking using Tabu search and an empirical estimate of binding affinity.

1 reference

12 December 2020

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

1 reference

12 December 2020

Structure-based discovery of inhibitors of thymidylate synthase

1 reference

12 December 2020

Mean field analysis of FKBP12 complexes with FK506 and rapamycin: implications for a role of crystallographic water molecules in molecular recognition and specificity

1 reference

12 December 2020

Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Hydrophobic docking: a proposed enhancement to molecular recognition techniques.

1 reference

12 December 2020

Protein-protein recognition: exploring the energy funnels near the binding sites.

1 reference

12 December 2020

A fast flexible docking method using an incremental construction algorithm.

1 reference

12 December 2020

Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization

1 reference

12 December 2020

Polymer principles and protein folding

1 reference

12 December 2020

Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

1 reference

12 December 2020

Three-dimensional structures of avidin and the avidin-biotin complex

1 reference

12 December 2020

Refined solution structures of the Escherichia coli trp holo- and aporepressor

1 reference

12 December 2020

Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking

1 reference

12 December 2020

Structure-based inhibitors of HIV-1 protease

1 reference

12 December 2020

Computation of the binding of fully flexible peptides to proteins with flexible side chains.

1 reference

12 December 2020

Molecular docking to ensembles of protein structures

1 reference

12 December 2020

A geometry-based suite of molecular docking processes

1 reference

12 December 2020

A multiple-start Monte Carlo docking method.

1 reference

12 December 2020

X-ray crystal structure of the Ala-109-->Thr variant of human transthyretin which produces euthyroid hyperthyroxinemia

1 reference

12 December 2020

Molecular docking towards drug discovery

1 reference

12 December 2020

Computational methods to predict binding free energy in ligand-receptor complexes

1 reference

12 December 2020

Molecular dynamics simulation of the docking of substrates to proteins.

1 reference

12 December 2020

Identifiers

DOI

10.1023/A:1008158231558

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11131967%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/VerkhivkerBGRACFLLMR00

3 November 2019

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1025748854

0 references

1 reference