Soft docking and multiple receptor conformations in virtual screening (Q41968000)

14 October 2017

Soft docking and multiple receptor conformations in virtual screening (English)

1 reference

14 October 2017

1 reference

Anna Maria Ferrari

1

1 reference

14 October 2017

Binqing Q Wei

series ordinal

2

1 reference

14 October 2017

Luca Costantino

series ordinal

3

1 reference

14 October 2017

Brian K Shoichet

series ordinal

4

1 reference

14 October 2017

language of work or name

English

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publication date

1 October 2004

1 reference

Journal of Medicinal Chemistry

14 October 2017

1 reference

14 October 2017

47

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14 October 2017

21

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14 October 2017

5076-5084

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

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A specific mechanism of nonspecific inhibition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A model binding site for testing scoring functions in molecular docking

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Protein-protein docking with multiple residue conformations and residue substitutions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

The structure of human recombinant aldose reductase complexed with the potent inhibitor zenarestat

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Soft protein-protein docking in internal coordinates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

FlexE: efficient molecular docking considering protein structure variations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Deciphering common failures in molecular docking of ligand-protein complexes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Developing a dynamic pharmacophore model for HIV-1 integrase.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Flexible ligand docking using conformational ensembles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

The alrestatin double-decker: binding of two inhibitor molecules to human aldose reductase reveals a new specificity determinant

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Molecular docking to ensembles of protein structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A geometric approach to macromolecule-ligand interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

N-[5-(trifluoromethyl)-6-methoxy-1-naphthalenyl]thioxomethyl]- N-methylglycine (Tolrestat), a potent, orally active aldose reductase inhibitor

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Efficient conformational sampling of local side-chain flexibility

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Ligand solvation in molecular docking.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Ligand docking to proteins with discrete side-chain flexibility.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413506

Synthesis, activity, and molecular modeling of a new series of tricyclic pyridazinones as selective aldose reductase inhibitors

18 August 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening

1 reference

12 December 2020

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

1 reference

12 December 2020

Identifiers

DOI

10.1021/JM049756P

1 reference

14 October 2017

1 reference

14 October 2017

1 reference