(Q28551247)

1

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Stefano Forli

2

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Arthur J Olson

4

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Michel F Sanner

PLOS Computational Biology

5

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language of work or name

English

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publication date

December 2015

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published in

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volume

11

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issue

12

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page(s)

e1004586

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copyright license

Creative Commons Attribution 4.0 International

start time

2 December 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Protein flexibility in docking and surface mapping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

19 March 2017

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=4667975

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

A semiempirical free energy force field with charge-based desolvation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Improved protein-ligand docking using GOLD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

GalaxyDock: protein-ligand docking with flexible protein side-chains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Advances and challenges in protein-ligand docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Successful applications of computer aided drug discovery: moving drugs from concept to the clinic

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Docking ligands into flexible and solvated macromolecules. 2. Development and application of fitted 1.5 to the virtual screening of potential HCV polymerase inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Current topics in computer-aided drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Protein-ligand docking with multiple flexible side chains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Virtual screening in drug discovery -- a computational perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Effective handling of induced-fit motion in flexible docking.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Blind docking of drug-sized compounds to proteins with up to a thousand residues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Discovery of a novel binding trench in HIV integrase.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

The many roles of computation in drug discovery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Blind docking of pharmaceutically relevant compounds using RosettaLigand

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4667975

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Minimization by Random Search Techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Diverse, high-quality test set for the validation of protein-ligand docking performance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Blind docking of 260 protein-ligand complexes with EADock 2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

The Hungarian method for the assignment problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004586

Identification of the sites of interaction between c-Raf-1 and Ras-GTP

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Hierarchical and multi-resolution representation of protein flexibility

1 reference

12 December 2020

Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1004586

Identifiers

DOI

0 references

DBLP publication ID

journals/ploscb/RavindranathFGO15

1 reference

DBLP Dataset 2021-01-02