(Q33327574)

25 July 2017

MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening (English)

1 reference

25 July 2017

Maria A Miteva

4

0 references

Bruno O Villoutreix

series ordinal

3

object named as

Bruno O Villoutreix

1 reference

25 July 2017

Nicolas Sauton

1

1 reference

PubMed ID

18402678

25 July 2017

David Lagorce

series ordinal

2

1 reference

25 July 2017

10 April 2008

1 reference

25 July 2017

1 reference

25 July 2017

9

1 reference

25 July 2017

184

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-9-184

25 July 2017

0 references

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Virtual screening strategies in drug discovery

28 July 2018

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Free resources to assist structure-based virtual ligand screening experiments

28 July 2018

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Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V

28 July 2018

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Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections

28 July 2018

1 reference

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Ligand docking and structure-based virtual screening in drug discovery

28 July 2018

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Frog: a FRee Online druG 3D conformation generator.

28 July 2018

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Shape variation in protein binding pockets and their ligands

28 July 2018

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Identification of nonpeptide CCR5 receptor agonists by structure-based virtual screening

28 July 2018

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Development and validation of a modular, extensible docking program: DOCK 5.

28 July 2018

1 reference

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A critical assessment of docking programs and scoring functions

28 July 2018

1 reference

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Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

28 July 2018

1 reference

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Shape Signatures: speeding up computer aided drug discovery

28 July 2018

1 reference

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FAF-Drugs: free ADME/tox filtering of compound collections.

28 July 2018

1 reference

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The interplay between structure-based design and combinatorial chemistry

28 July 2018

1 reference

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Structure-based development of target-specific compound libraries

28 July 2018

1 reference

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Optimizing the use of open-source software applications in drug discovery

28 July 2018

1 reference

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Hierarchical docking of databases of multiple ligand conformations

28 July 2018

1 reference

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RPBS: a web resource for structural bioinformatics

28 July 2018

1 reference

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Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates

28 July 2018

1 reference

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Virtual screening of chemical libraries

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Docking and scoring in virtual screening for drug discovery: methods and applications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

NMRShiftDB – compound identification and structure elucidation support through a free community-built web database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Virtual screening methods that complement HTS.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Evaluation of docking performance: comparative data on docking algorithms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Implications of protein flexibility for drug discovery

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Gaussian docking functions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Inhibition of protein-protein association by small molecules: approaches and progress

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

28 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

A geometric approach to macromolecule-ligand interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Receptor-based computational screening of compound databases: the main docking-scoring engines

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

Identification of Ellagic Acid as Potent Inhibitor of Protein Kinase CK2: A Successful Example of a Virtual Screening Application

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373571

How Reliable Are Current Docking Approaches for Structure-Based Drug Design? Lessons from Aldose Reductase

31 October 2018

1 reference

12 December 2020

Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools

1 reference

12 December 2020

Validation and use of the MM-PBSA approach for drug discovery

1 reference

12 December 2020

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-9-184

1 reference

journals/bmcbi/SautonLVM08

25 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

25 July 2017

1 reference

PubMed ID

18402678