Hierarchical docking of databases of multiple ligand conformations (Q24538548)

6 July 2017

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title

Hierarchical docking of databases of multiple ligand conformations (English)

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6 July 2017

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Brian K

Shoichet

Brian K Shoichet

1 reference

6 July 2017

David M Lorber

David M

Lorber

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6 July 2017

language of work or name

English

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publication date

1 January 2005

1 reference

Current Topics in Medicinal Chemistry

6 July 2017

published in

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6 July 2017

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6 July 2017

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6 July 2017

page(s)

739-749

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Flexible ligand docking using conformational ensembles

6 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase

24 March 2017

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

24 March 2017

1 reference

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Structure-based design of submicromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Development and validation of a genetic algorithm for flexible docking

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Automated docking of flexible ligands: applications of AutoDock

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Dominant forces in protein folding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Here be dragons: docking and screening in an uncharted region of chemical space

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Testing a flexible-receptor docking algorithm in a model binding site

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Current trends in lead discovery: are we looking for the appropriate properties?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Simple selection criteria for drug-like chemical matter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

FlexE: efficient molecular docking considering protein structure variations.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Pharmacophore fingerprinting. 2. Application to primary library design

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

DREAM++: flexible docking program for virtual combinatorial libraries

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Recognizing molecules with drug-like properties

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Can we learn to distinguish between "drug-like" and "nondrug-like" molecules?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

A geometric approach to macromolecule-ligand interactions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Soft docking and multiple receptor conformations in virtual screening

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Exhaustive docking of molecular fragments with electrostatic solvation.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Flexible ligand docking using a genetic algorithm.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Monte Carlo docking of oligopeptides to proteins.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

FlexX-Scan: fast, structure-based virtual screening

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Protein flexibility in ligand docking and virtual screening to protein kinases.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

ICM-DISCO docking by global energy optimization with fully flexible side-chains

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Excluded volume in protein side-chain packing.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Improving the odds in discriminating "drug-like" from "non drug-like" compounds.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

DARWIN: a program for docking flexible molecules.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

SQ: a program for rapidly producing pharmacophorically relevent molecular superpositions.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

A fast flexible docking method using an incremental construction algorithm.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1364474

A family competition evolutionary algorithm for automated docking of flexible ligands to proteins

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16101414

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of electrostatic potentials in an enzyme active site

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16101414

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.2174/1568026054637683

1 reference

release_seo7jpqlwzf7lp3k6b7wd7llzi

6 July 2017

Fatcat ID

0 references

PMC publication ID

1364474

1 reference

6 July 2017

1 reference