DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases (Q27231136)

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

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English	DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases	scientific article	DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases

Statements

instance of

scholarly article

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title

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

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main subject

molecular modelling

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automation

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database

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docking

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based on heuristic

inferred from title

author name string

T J Ewing

series ordinal

1

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S Makino

series ordinal

2

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A G Skillman

series ordinal

3

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I D Kuntz

series ordinal

4

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language of work or name

English

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publication date

May 2001

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published in

Journal of Computer - Aided Molecular Design

publication date

May 2001

volume

15

issue

5

page(s)

411–428

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volume

15

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issue

5

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page(s)

411-28

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cites work

Flexible ligand docking using a genetic algorithm.

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12 December 2020

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

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A comparison of heuristic search algorithms for molecular docking.

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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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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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reference URL

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based on heuristic

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Development and validation of a genetic algorithm for flexible docking

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High-resolution structure of the complex between carboxypeptidase A andL-phenyl lactate

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Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases

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A geometric approach to macromolecule-ligand interactions

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Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

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A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors

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Docking of hydrophobic ligands with interaction-based matching algorithms.

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Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors

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Q27676822

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based on heuristic

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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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Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

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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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based on heuristic

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A fast flexible docking method using an incremental construction algorithm.

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/11394736

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature

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PubMed

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/11394736

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular docking to ensembles of protein structures

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/11394736

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Matching chemistry and shape in molecular docking

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/11394736

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes

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stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/11394736

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/11394736

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1023/A:1011115820450

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1696699

DBLP publication ID

journals/jcamd/EwingMSK01

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

Dimensions Publication ID

1024234487

0 references

OpenCitations bibliographic resource ID

1696699

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1696699

PubMed publication ID

11394736

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1696699

ResearchGate publication ID

11944272

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