(Q34937524)

5 August 2017

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title

A review of protein-small molecule docking methods (English)

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5 August 2017

Taylor RD

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5 August 2017

Jewsbury PJ

series ordinal

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5 August 2017

Essex JW

series ordinal

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5 August 2017

publication date

1 March 2002

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Journal of Computer - Aided Molecular Design

5 August 2017

published in

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5 August 2017

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5 August 2017

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5 August 2017

page(s)

151-166

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A fast and efficient method to generate biologically relevant conformations

5 August 2017

cites work

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12 December 2020

CASP2 molecular docking predictions with the LIGIN software

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12 December 2020

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A comparison of heuristic search algorithms for molecular docking.

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Structure-based strategies for drug design and discovery

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The particle concept: placing discrete water molecules during protein-ligand docking predictions.

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Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

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Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

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

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CONCERTS: dynamic connection of fragments as an approach to de novo ligand design

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BUILDER v.2: improving the chemistry of a de novo design strategy

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Structural origins of high-affinity biotin binding to streptavidin

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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

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12 December 2020

Molecular docking using surface complementarity.

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

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

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Ligand docking to proteins with discrete side-chain flexibility.

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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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12 December 2020

An example of a protein ligand found by database mining: description of the docking method and its verification by a 2.3 A X-ray structure of a thrombin-ligand complex.

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Development and validation of a genetic algorithm for flexible docking

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Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

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12 December 2020

Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies

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Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation.

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Flexible ligand docking using conformational ensembles

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Modelling protein docking using shape complementarity, electrostatics and biochemical information

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The computer program LUDI: a new method for the de novo design of enzyme inhibitors

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Accommodating protein flexibility in computational drug design

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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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A geometric approach to macromolecule-ligand interactions

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Flexible ligand docking: a multistep strategy approach

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12 December 2020

Predictive docking of protein-protein and protein-DNA complexes.

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New approach to molecular docking and its application to virtual screening of chemical databases

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Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

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QXP: powerful, rapid computer algorithms for structure-based drug design

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Protein-protein recognition

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

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Predicting the structure of protein complexes: a step in the right direction

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

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Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

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

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Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

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De novo design of enzyme inhibitors by Monte Carlo ligand generation

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FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure

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

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Optimal protocol and trajectory visualization for conformational searches of peptides and proteins

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DARWIN: a program for docking flexible molecules

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12 December 2020

Receptor-induced conformation change of the immunosuppressant cyclosporin A.

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12 December 2020

Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads

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12 December 2020

The dead-end elimination theorem and its use in protein side-chain positioning

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12 December 2020

MCDOCK: a Monte Carlo simulation approach to the molecular docking problem

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12 December 2020

High-throughput docking for lead generation

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12 December 2020

FlexE: efficient molecular docking considering protein structure variations.

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12 December 2020

Automated docking of substrates to proteins by simulated annealing

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12 December 2020

SPROUT: a program for structure generation.

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12 December 2020

LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

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12 December 2020

A fast flexible docking method using an incremental construction algorithm.

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12 December 2020

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

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12 December 2020

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

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12 December 2020

GroupBuild: a fragment-based method for de novo drug design

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12 December 2020

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

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12 December 2020

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

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12 December 2020

Molecular docking to ensembles of protein structures

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12 December 2020

The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase

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12 December 2020

Two-stage method for protein-ligand docking

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12 December 2020

Rational automatic search method for stable docking models of protein and ligand.

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12 December 2020

A multiple-start Monte Carlo docking method.

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12 December 2020

GenStar: a method for de novo drug design.

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12 December 2020

"Soft docking": matching of molecular surface cubes

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12 December 2020

Molecular dynamics simulation of the docking of substrates to proteins.

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12 December 2020

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

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12 December 2020

Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin.

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12 December 2020

Identifiers

DOI

10.1023/A:1020155510718

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journals/jcamd/TaylorJE02

5 August 2017

DBLP publication ID

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DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1007856005

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