Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database (Q51664708)

9 April 2018

title

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

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9 April 2018

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Krzysztof Ginalski

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9 April 2018

Dariusz Plewczynski

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object named as

Dariusz Plewczynski

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9 April 2018

Michal Lazniewski

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Michał Łaźniewski

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9 April 2018

author name string

Rafał Augustyniak

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9 April 2018

publication date

1 September 2010

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9 April 2018

Journal of Computational Chemistry

published in

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9 April 2018

volume

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9 April 2018

issue

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9 April 2018

page(s)

742-755

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9 April 2018

Ligand.Info small-molecule Meta-Database.

cites work

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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Convergence and combination of methods in protein-protein docking

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Principles of flexible protein-protein docking

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Recent Progress and Future Directions in Protein-Protein Docking

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Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex

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Molecular docking to ensembles of protein structures

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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

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A fast flexible docking method using an incremental construction algorithm.

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

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Development and validation of a genetic algorithm for flexible docking

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ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

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Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

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Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

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

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Comparative study of several algorithms for flexible ligand docking

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Evaluation of docking performance: comparative data on docking algorithms

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Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography

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Comparative assessment of scoring functions on a diverse test set.

21 January 2018

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An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes

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Consensus scoring with feature selection for structure-based virtual screening

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SeleX-CS: a new consensus scoring algorithm for hit discovery and lead optimization

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eHiTS: a new fast, exhaustive flexible ligand docking system

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General and targeted statistical potentials for protein-ligand interactions.

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A fast and efficient method to generate biologically relevant conformations

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

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Methodological developments and strategies for a fast flexible superposition of drug-size molecules

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

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eHiTS: an innovative approach to the docking and scoring function problems.

21 January 2018

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Automated docking with grid-based energy evaluation

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Comparative evaluation of 11 scoring functions for molecular docking

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Evaluation of docking functions for protein-ligand docking

21 January 2018

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

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Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

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21 January 2018

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The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes.

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21 January 2018

Identifiers

DOI

10.1002/JCC.21643

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9 April 2018

journals/jcc/PlewczynskiLAG11

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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9 April 2018