Variability in docking success rates due to dataset preparation (Q36095634)

12 August 2017

Variability in docking success rates due to dataset preparation (English)

1 reference

12 August 2017

1 reference

Christopher R Corbeil

series ordinal

1

1 reference

12 August 2017

Christopher I Williams

series ordinal

2

1 reference

12 August 2017

Paul Labute

series ordinal

3

1 reference

12 August 2017

8 May 2012

1 reference

Journal of Computer - Aided Molecular Design

12 August 2017

1 reference

12 August 2017

26

1 reference

12 August 2017

6

1 reference

12 August 2017

775-786

1 reference

Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction (CASP)--round IX

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Challenges and advances in computational docking: 2009 in review

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Advances and Challenges in Protein-Ligand Docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

The role of water molecules in computational drug design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking screens: right for the right reasons?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Structural and Functional Analysis of Campylobacter jejuni PseG: A UDP-SUGAR HYDROLASE FROM THE PSEUDAMINIC ACID BIOSYNTHETIC PATHWAY

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Unraveling water's entropic mysteries: a unified view of nonpolar, polar, and ionic hydration

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Exploiting ordered waters in molecular docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Recommendations for evaluation of computational methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Modeling of metal interaction geometries for protein-ligand docking.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction-Round VII

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking and scoring protein complexes: CAPRI 3rd Edition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Water at biomolecular binding interfaces

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Benchmarking sets for molecular docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

A critical assessment of docking programs and scoring functions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction (CASP)--round 6.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction (CASP)-round V.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction (CASP): round IV.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

2 October 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=3397132

Critical assessment of methods of protein structure prediction (CASP): round III.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction (CASP): round II.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Development and validation of a genetic algorithm for flexible docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

A large-scale experiment to assess protein structure prediction methods.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking and scoring protein interactions: CAPRI 2009

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

The SAMPL2 blind prediction challenge: introduction and overview

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Structure-activity relationship of novel DAPK inhibitors identified by structure-based virtual screening

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Critical assessment of methods of protein structure prediction - Round VIII.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Predictions of binding for dopamine D2 receptor antagonists by the SIE method

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Docking of aminoglycosides to hydrated and flexible RNA.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Modeling water molecules in protein-ligand docking using GOLD.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Assessment of blind predictions of protein-protein interactions: current status of docking methods

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Comparative evaluation of 11 scoring functions for molecular docking

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3397132

Interdomain Interactions Modulate Collective Dynamics of the Metal-Binding Domains in the Wilson Disease Protein

21 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007/S10822-012-9570-1

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

21 January 2018

1 reference

12 December 2020

Reducing docking score variations arising from input differences

1 reference

12 December 2020

Computer-aided drug design platform using PyMOL

1 reference

12 December 2020

Effect of input differences on the results of docking calculations

1 reference

12 December 2020

The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area

1 reference

12 December 2020

10.1007/S10822-012-9570-1

Identifiers

DOI

1 reference

journals/jcamd/CorbeilWL12

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 August 2017

PubMed publication ID

22566074

1 reference