Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking (Q42251037)

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scientific article published on 5 July 2012

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

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English	Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking	scientific article published on 5 July 2012	Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

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scholarly article

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5 February 2020

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking (English)

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5 February 2020

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5 February 2020

author name string

Michael M Mysinger

1

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5 February 2020

Michael Carchia

2

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5 February 2020

Brian K Shoichet

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5 February 2020

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5 July 2012

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5 February 2020

Journal of Medicinal Chemistry

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5 February 2020

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5 February 2020

6582-6594

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5 February 2020

14

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5 February 2020

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

1 reference

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Evaluation of DOCK 6 as a pose generation and database enrichment tool

1 reference

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26 October 2017

Lead Finder docking and virtual screening evaluation with Astex and DUD test sets

1 reference

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26 October 2017

Docking and scoring with ICM: the benchmarking results and strategies for improvement

1 reference

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26 October 2017

Surflex-Dock: Docking benchmarks and real-world application

1 reference

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DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.

1 reference

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Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4

1 reference

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Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

1 reference

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26 October 2017

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

1 reference

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26 October 2017

How to benchmark methods for structure-based virtual screening of large compound libraries

1 reference

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Ligand and decoy sets for docking to G protein-coupled receptors

1 reference

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ChEMBL: a large-scale bioactivity database for drug discovery

1 reference

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Ligand discovery from a dopamine D3 receptor homology model and crystal structure

1 reference

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26 October 2017

DEKOIS: demanding evaluation kits for objective in silico screening--a versatile tool for benchmarking docking programs and scoring functions

1 reference

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26 October 2017

Complementarity Between a Docking and a High-Throughput Screen in Discovering New Cruzain Inhibitors

1 reference

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26 October 2017

Structure-based discovery of A2A adenosine receptor ligands

1 reference

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26 October 2017

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database

1 reference

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26 October 2017

Molecular docking screens using comparative models of proteins

1 reference

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26 October 2017

Automated docking screens: a feasibility study

1 reference

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26 October 2017

Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data

1 reference

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26 October 2017

Docking for fragment inhibitors of AmpC -lactamase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Structure-based discovery of beta2-adrenergic receptor ligands

1 reference

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26 October 2017

Recommendations for evaluation of computational methods

1 reference

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26 October 2017

Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Community benchmarks for virtual screening

1 reference

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26 October 2017

How to do an evaluation: pitfalls and traps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Benchmarking sets for molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Parameter estimation for scoring protein-ligand interactions using negative training data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Decoys for docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

ZINC--a free database of commercially available compounds for virtual screening

1 reference

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26 October 2017

E-MSD: an integrated data resource for bioinformatics

1 reference

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26 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

1 reference

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26 October 2017

UniProt: the Universal Protein knowledgebase

1 reference

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26 October 2017

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation

1 reference

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26 October 2017

Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase

1 reference

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26 October 2017

Detailed analysis of scoring functions for virtual screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

The Protein Data Bank

1 reference

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26 October 2017

The maximal affinity of ligands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

The properties of known drugs. 1. Molecular frameworks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

26 October 2017

REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

29 May 2018

Bias, reporting, and sharing: computational evaluations of docking methods

1 reference

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29 May 2018

Virtual decoy sets for molecular docking benchmarks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

17 August 2018

Rapid context-dependent ligand desolvation in molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

17 August 2018

Assessing scoring functions for protein-ligand interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405771

17 August 2018

Virtual screening using protein-ligand docking: avoiding artificial enrichment.

1 reference

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17 August 2018

Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

1 reference

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17 August 2018

Comparison of Shape-Matching and Docking as Virtual Screening Tools

1 reference

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1 December 2018

Can we use docking and scoring for hit-to-lead optimization?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22716043

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Better than random? The chemotype enrichment problem

1 reference

https://pubmed.ncbi.nlm.nih.gov/22716043

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JM300687E

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Europe PubMed Central

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5 February 2020

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Europe PubMed Central

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5 February 2020

1 reference

Europe PubMed Central

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5 February 2020

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