High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations (Q28476233)

1

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Noriyuki Futatsugi

2

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Hideyoshi Fuji

3

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Atsushi Suenaga

4

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Gentaro Morimoto

5

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Ryoko Yanai

6

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Yousuke Ohno

7

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Tetsu Narumi

PLOS Computational Biology

8

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language of work or name

English

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publication date

October 2009

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published in

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volume

5

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issue

10

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page(s)

e1000528

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copyright license

Creative Commons Attribution 4.0 International

start time

9 October 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Fragment-based lead discovery: leads by design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme)

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Molecular recognition of cyclic urea HIV-1 protease inhibitors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Development and validation of a genetic algorithm for flexible docking

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Automated docking of flexible ligands: applications of AutoDock

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Development and testing of a general amber force field

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Benchmarking sets for molecular docking

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Reduced surface: an efficient way to compute molecular surfaces

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

A fragment-based approach for the discovery of isoform-specific p38alpha inhibitors

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Protein structures in virtual screening: a case study with CDK2.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Monte Carlo validation of the Dorfman-Berbaum-Metz method using normalized pseudovalues and less data-based model simplification

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

The PDBbind database: methodologies and updates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

A comparison of the Dorfman-Berbaum-Metz and Obuchowski-Rockette methods for receiver operating characteristic (ROC) data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Comparative study of several algorithms for flexible 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=2746282

Evaluation of docking performance: comparative data on docking algorithms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Ligand binding affinities from MD simulations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand 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=2746282

Molecular complexity and its impact on the probability of finding leads for 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=2746282

Detailed analysis of scoring functions for virtual screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Two-stage method for 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=2746282

A high-throughput fluorescence screen to monitor the specific binding of antagonists to RNA targets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Dorfman-Berbaum-Metz method for statistical analysis of multireader, multimodality receiver operating characteristic data: validation with computer simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Computational approaches to molecular recognition.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

A Homogenous 384-Well High Throughput Screen for Novel Tumor Necrosis Factor Receptor: Ligand Interactions Using Time Resolved Energy Transfer

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Comparative evaluation of 11 scoring functions for molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

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.1000528

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Evaluating the Accuracy of the Quasiharmonic Approximation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Ultra-high throughput screen of two-million-member combinatorial compound collection in a miniaturized, 1536-well assay format

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Receiver Operating Characteristic Rating Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000528

Conformational entropy of biomolecules: beyond the quasi-harmonic approximation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

Receiver operating characteristic rating analysis. Generalization to the population of readers and patients with the jackknife method

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746282

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

27 November 2018

1 reference

12 December 2020

New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2

1 reference

12 December 2020

Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen

1 reference

12 December 2020

Variance-component modeling in the analysis of receiver operating characteristic index estimates

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000528

Identifiers

DOI

1 reference

journals/ploscb/OkimotoFFSMYONT09

286322

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_axmdksi4djgodkwkf35ofijxla

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/axmdksi4djgodkwkf35ofijxla

24 November 2022

mapped directly with Wikidata item

286322

1 reference

1 reference

1 reference