Surflex-Dock: Docking benchmarks and real-world application.

Journal of Computer-aided Molecular Design
Russell Spitzer, A N Jain

Abstract

Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by emp...Continue Reading

References

Jan 1, 1990·Proteins·D S Goodsell, A J Olson
Oct 25, 1982·Journal of Molecular Biology·I D KuntzT E Ferrin
Jan 1, 1996·Journal of Molecular Recognition : JMR·D S GoodsellA J Olson
Aug 23, 1996·Journal of Molecular Biology·M RareyG Klebe
Mar 1, 1997·Protein Science : a Publication of the Protein Society·J RuppertA N Jain
Apr 4, 1997·Journal of Molecular Biology·G JonesR Taylor
Feb 12, 2002·Bioinformatics·Xi ChenMichael K Gilson
Feb 6, 2004·Journal of Medicinal Chemistry·Ajay N Jain
Mar 19, 2004·Journal of Medicinal Chemistry·Richard A FriesnerPeter S Shenkin
Mar 19, 2004·Journal of Medicinal Chemistry·Thomas A HalgrenJay L Banks
May 12, 2006·Journal of Medicinal Chemistry·Ann E Cleves, Ajay N Jain
Sep 29, 2006·Journal of Medicinal Chemistry·Tuan A Pham, Ajay N Jain
Sep 29, 2006·Journal of Medicinal Chemistry·Gregory L WarrenMartha S Head
Dec 13, 2006·Journal of Medicinal Chemistry·Niu HuangJohn J Irwin
Jan 5, 2007·Journal of Medicinal Chemistry·Paul C D HawkinsAnthony Nicholls
Feb 16, 2007·Journal of Medicinal Chemistry·Michael J HartshornChristopher W Murray
Oct 25, 2007·Journal of Chemical Information and Modeling·Jeffrey J SutherlandMichal Vieth
Dec 13, 2007·Journal of Computer-aided Molecular Design·Ann E Cleves, Ajay N Jain
Dec 14, 2007·Journal of Computer-aided Molecular Design·Ajay N Jain
Mar 14, 2008·Journal of Computer-aided Molecular Design·Ajay N Jain, Anthony Nicholls
Oct 29, 2008·Journal of Chemical Information and Modeling·Marcel L VerdonkChristopher W Murray
May 30, 2009·Journal of Chemical Information and Modeling·Jason B CrossChristine Humblet
Jun 6, 2009·Nucleic Acids Research·Yanli WangStephen H Bryant
Feb 18, 2010·Journal of Medicinal Chemistry·Anthony NichollsBrian Kelley
Jul 20, 2011·Proteins·Russell SpitzerAjay N Jain

❮ Previous
Next ❯

Citations

Nov 12, 2013·Journal of Computer-aided Molecular Design·Rocco VarelaAjay N Jain
Jul 31, 2013·Quarterly Reviews of Biophysics·Alexey V Onufriev, Emil Alexov
Jul 7, 2012·Journal of Chemical Information and Modeling·Álvaro Cortés CabreraAntonio Morreale
Jun 24, 2014·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Yang LiuJan Balzarini
Mar 1, 2014·Future Medicinal Chemistry·Prashant S KharkarRam S Gaud
Feb 11, 2016·Journal of Computer-aided Molecular Design·Ann E Cleves, Ajay N Jain
Dec 30, 2015·Journal of Agricultural and Food Chemistry·Zhong-lin MaFan-hong Wu
Jun 22, 2012·Journal of Medicinal Chemistry·Michael M MysingerBrian K Shoichet
Oct 1, 2015·Journal of Chemical Information and Modeling·Richard D SmithHeather A Carlson
Feb 20, 2013·Journal of Computational Chemistry·Marcel Schumann, Roger S Armen
Oct 30, 2013·Proteins·Russell SpitzerAjay N Jain
Mar 22, 2016·International Journal of Molecular Sciences·Xing WangYanjiang Qiao
May 4, 2015·European Journal of Medicinal Chemistry·Zheng-Yong WanChristophe Pannecouque
Mar 27, 2015·Journal of Molecular Recognition : JMR·Elizabeth YurievPaul A Ramsland
May 6, 2015·Journal of Computer-aided Molecular Design·Ann E Cleves, Ajay N Jain
Sep 23, 2014·Journal of Molecular Graphics & Modelling·Lan-Lan ZangRun-Ling Wang
Jan 1, 2013·Computational and Structural Biotechnology Journal·Valère LounnasNicolas Foloppe
Dec 30, 2014·Trends in Pharmacological Sciences·Yu-Chian Chen
Nov 28, 2014·Journal of Computer-aided Molecular Design·Ann E Cleves, Ajay N Jain
Jun 28, 2016·Journal of Chemical Information and Modeling·Heather A Carlson
Dec 17, 2016·Journal of Chemical Information and Modeling·Prasad ChaskarUte F Röhrig
Dec 21, 2016·Future Medicinal Chemistry·Shangying ChenWai Keung Chui
Apr 29, 2016·PLoS Computational Biology·Tatiana MaximovaAmarda Shehu
Nov 13, 2015·Memórias do Instituto Oswaldo Cruz·Lucianna Helene SantosErnesto Raúl Caffarena
Jun 18, 2017·Journal of Computer-aided Molecular Design·Minkyung BaekChaok Seok
Apr 4, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Zhen-Peng KaiShan-Shan Chen
Oct 11, 2013·Journal of Computational Chemistry·Woong-Hee ShinChaok Seok

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.