Surflex-Dock: Docking benchmarks and real-world application (Q36098724)

12 August 2017

Surflex-Dock: Docking benchmarks and real-world application (English)

1 reference

12 August 2017

Russell Spitzer

1 reference

12 August 2017

Ajay N Jain

series ordinal

1 reference

12 August 2017

language of work or name

1 reference

9 May 2012

1 reference

Journal of Computer - Aided Molecular Design

12 August 2017

1 reference

12 August 2017

1 reference

12 August 2017

1 reference

12 August 2017

687-699

1 reference

Molecular Shape and Medicinal Chemistry: A Perspective

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

PubChem: a public information system for analyzing bioactivities of small molecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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=3398190

Lessons in molecular recognition. 2. Assessing and improving cross-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=3398190

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=3398190

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=3398190

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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=3398190

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=3398190

The Binding Database: data management and interface 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=3398190

Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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=3398190

Automatic identification and representation of protein binding sites 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=3398190

Automated docking of flexible ligands: applications of AutoDock

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

A geometric approach to macromolecule-ligand interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Automated docking of substrates to proteins by simulated annealing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Surface-based protein binding pocket similarity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Novel inhibitors of poly(ADP-ribose) polymerase/PARP1 and PARP2 identified using a cell-based screen in yeast

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Protein-ligand docking against non-native protein conformers

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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=3398190

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=3398190

Robust ligand-based modeling of the biological targets of known drugs

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Ligand-based structural hypotheses for 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=3398190

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

A fast flexible docking method using an incremental construction algorithm.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398190

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

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-011-9533-Y

Comparison of Shape-Matching and Docking as Virtual Screening Tools

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-011-9533-Y

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22569590

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-011-9533-Y

1 reference

journals/jcamd/SpitzerJ12

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 August 2017

PubMed publication ID

22569590

1 reference