Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. (Q38390892)

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3 March 2020

review article

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title

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review (English)

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3 March 2020

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3

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3 March 2020

Elizabeth Yuriev

series ordinal

1

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3 March 2020

2

Jessica Holien

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3 March 2020

2 September 2017

publication date

21 March 2015

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Journal of Molecular Recognition

3 March 2020

published in

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3 March 2020

volume

28

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issue

10

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3 March 2020

page(s)

581-604

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Protein-ligand docking in the new millennium--a retrospective of 10 years in the field

3 March 2020

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Combining in silico and biophysical methods for the development of Pseudomonas aeruginosa quorum sensing inhibitors: an alternative approach for structure-based drug design

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Accounting for conformational variability in protein-ligand docking with NMR-guided rescoring

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Accessible high-throughput virtual screening molecular docking software for students and educators

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One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade

21 January 2018

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Virtual compound screening in drug discovery

21 January 2018

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Analysis of structure-based virtual screening studies and characterization of identified active compounds

21 January 2018

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Recognizing pitfalls in virtual screening: a critical review

21 January 2018

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Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery.

21 January 2018

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A performance/cost model for a CUDA drug discovery application on physical and public cloud infrastructures

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High-Throughput parallel blind Virtual Screening using BINDSURF.

21 January 2018

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Fast docking on graphics processing units via Ray-Casting

21 January 2018

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Fast force field-based optimization of protein-ligand complexes with graphics processor

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ZINC: a free tool to discover chemistry for biology

21 January 2018

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Broad coverage of commercially available lead-like screening space with fewer than 350,000 compounds

21 January 2018

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

21 January 2018

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Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets

21 January 2018

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

21 January 2018

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A critical assessment of docking programs and scoring functions

21 January 2018

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CSAR data set release 2012: ligands, affinities, complexes, and docking decoys

21 January 2018

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Check your confidence: size really does matter

21 January 2018

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CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series

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Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource benchmark

21 January 2018

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Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise

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Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark

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Application of the docking program SOL for CSAR benchmark

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

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Ligand pose and orientational sampling in molecular docking

21 January 2018

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Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41

21 January 2018

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Assessing molecular docking tools for relative biological activity prediction: a case study of triazole HIV-1 NNRTIs

21 January 2018

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Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation

21 January 2018

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Beware of machine learning-based scoring functions-on the danger of developing black boxes

21 January 2018

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BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures

21 January 2018

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QuickVina: accelerating AutoDock Vina using gradient-based heuristics for global optimization

21 January 2018

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Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.

21 January 2018

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A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

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AMMOS software: method and application

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21 January 2018

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Analysis of protein binding sites by computational solvent mapping

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FTSite: high accuracy detection of ligand binding sites on unbound protein structures

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pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring

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New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays

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e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design.

21 January 2018

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An integrated virtual screening approach for VEGFR-2 inhibitors

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Enrichment of virtual hits by progressive shape-matching and docking

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Development and evaluation of an integrated virtual screening strategy by combining molecular docking and pharmacophore searching based on multiple protein structures

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How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials

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21 January 2018

Identifiers

DOI

10.1002/JMR.2471

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25808539 AND SRC:MED&resulttype=core&format=json

3 March 2020

1 reference