A review of protein-small molecule docking methods (Q34937524)

5 August 2017

1 reference

title

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

1 reference

5 August 2017

Taylor RD

1

1 reference

5 August 2017

Jewsbury PJ

series ordinal

2

1 reference

5 August 2017

Essex JW

series ordinal

3

1 reference

5 August 2017

publication date

1 March 2002

1 reference

Journal of Computer - Aided Molecular Design

5 August 2017

published in

1 reference

5 August 2017

volume

16

1 reference

5 August 2017

issue

3

1 reference

5 August 2017

page(s)

151-166

1 reference

A fast and efficient method to generate biologically relevant conformations

5 August 2017

cites work

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

CASP2 molecular docking predictions with the LIGIN software

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Ligand—protein docking and rational drug design

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

A comparison of heuristic search algorithms for molecular docking.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Structure-based strategies for drug design and discovery

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Ligand-receptor docking with the Mining Minima optimizer.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Structural origins of high-affinity biotin binding to streptavidin

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Monte Carlo docking of oligopeptides to proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Computer design of bioactive molecules: a method for receptor-based de novo ligand design

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Molecular docking using surface complementarity.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Ligand docking to proteins with discrete side-chain flexibility.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

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.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Development and validation of a genetic algorithm for flexible docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Flexible ligand docking using conformational ensembles

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Modelling protein docking using shape complementarity, electrostatics and biochemical information

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Accommodating protein flexibility in computational drug design

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

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

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

A geometric approach to macromolecule-ligand interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Flexible ligand docking: a multistep strategy approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Protein-protein recognition

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

De novo design of enzyme inhibitors by Monte Carlo ligand generation

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

DARWIN: a program for docking flexible molecules.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Receptor-induced conformation change of the immunosuppressant cyclosporin A.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

High-throughput docking for lead generation

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

FlexE: efficient molecular docking considering protein structure variations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Automated docking of substrates to proteins by simulated annealing

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

SPROUT: a program for structure generation.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

A fast flexible docking method using an incremental construction algorithm.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Molecular docking to ensembles of protein structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Two-stage method for protein-ligand docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

A multiple-start Monte Carlo docking method.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

GenStar: a method for de novo drug design.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

"Soft docking": matching of molecular surface cubes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Molecular dynamics simulation of the docking of substrates to proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/12363215

12 December 2020

Identifiers

DOI

10.1023/A:1020155510718

1 reference

journals/jcamd/TaylorJE02

5 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1007856005

0 references

1 reference