Rapid flexible docking using a stochastic rotamer library of ligands (Q33659311)

28 July 2017

Rapid flexible docking using a stochastic rotamer library of ligands (English)

1 reference

28 July 2017

1 reference

Shuangye Yin

2

0 references

Feng Ding

object named as

Feng Ding

series ordinal

1

0 references

Nikolay V. Dokholyan

object named as

Nikolay V Dokholyan

series ordinal

3

0 references

publication date

1 September 2010

1 reference

Journal of Chemical Information and Modeling

28 July 2017

1 reference

28 July 2017

50

1 reference

28 July 2017

9

1 reference

28 July 2017

1623-1632

1 reference

Molecular docking screens using comparative models of proteins

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Blind docking of pharmaceutically relevant compounds using RosettaLigand

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

MedusaScore: an accurate force field-based scoring function for virtual drug screening

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

A simple model of backbone flexibility improves modeling of side-chain conformational variability

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Modeling backbone flexibility improves protein stability estimation.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

A flexible approach to induced fit docking

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Exploring experimental sources of multiple protein conformations in structure-based drug design.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Benchmarking sets for molecular docking

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Protein-ligand docking: current status and future challenges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Emergence of protein fold families through rational design

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Novel procedure for modeling ligand/receptor induced fit effects.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Molecular dynamics and protein function

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Conformational flexibility models for the receptor in structure based drug design.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Implications of protein flexibility for drug discovery

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Molecular dynamics of biological macromolecules: a brief history and perspective

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Accommodating protein flexibility in computational drug design

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

14 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=2947618

Molecular docking to ensembles of protein structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

RosettaLigand docking with full ligand and receptor flexibility.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Fully automated molecular mechanics based induced fit protein-ligand docking method.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Eris: an automated estimator of protein stability.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Fully flexible low-mode docking: application to induced fit in HIV integrase.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2947618

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20712341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Assessing the performance of OMEGA with respect to retrieving bioactive conformations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20712341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of electrostatic interactions in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20712341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI100218T

1 reference

28 July 2017

journals/jcisd/DingYD10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

28 July 2017

1 reference

PubMed ID

20712341