Consensus scoring for protein-ligand interactions

Drug Discovery Today
Miklos Feher

Abstract

This article reviews the application of consensus scoring for cases when the target 3D structure is known. Comparing the performance of different methods is not a trivial task, and it appears that consensus scoring usually substantially improves virtual screening performance, contributing to better enrichments. It also seems to improve--albeit less dramatically--the prediction of bound conformations and poses. The prediction of binding energies is still rather inaccurate and although consensus scoring generally improves these predictions, more development is required before it can be used for this purpose in routine lead optimization.

References

Apr 12, 2001·Journal of Medicinal Chemistry·M Stahl, M Rarey
Oct 18, 2001·Journal of Chemical Information and Computer Sciences·R Wang, S Wang
Feb 23, 2002·Journal of Molecular Graphics & Modelling·Robert D ClarkJames B Matthew
Jan 28, 2003·Drug Discovery Today·Paul D Lyne
May 30, 2003·Journal of Medicinal Chemistry·Renxiao WangShaomeng Wang
Dec 12, 2003·Journal of Medicinal Chemistry·Micael JacobssonUlf Norinder
Mar 6, 2004·Journal of Molecular Biology·Claudio N Cavasotto, Ruben A Abagyan
Mar 20, 2004·Science·William L Jorgensen
May 25, 2004·Journal of Chemical Information and Computer Sciences·Eva M Krovat, Thierry Langer
Aug 24, 2004·Combinatorial Chemistry & High Throughput Screening·Mark AshtonMark Whittaker
Nov 3, 2004·Nature Reviews. Drug Discovery·Douglas B KitchenJürgen Bajorath
Nov 10, 2004·Organic & Biomolecular Chemistry·Philip M MarsdenRobert C Glen
Dec 15, 2004·Journal of Computer-aided Molecular Design·Li XingDavid Sedlock
Jan 26, 2005·Journal of Chemical Information and Modeling·Zhenming LiuLuhua Lai
Feb 18, 2005·Journal of Medicinal Chemistry·Maxwell D CummingsEdward P Jaeger
Feb 23, 2005·Current Pharmaceutical Design·Venkatraman MohanRenee L DesJarlais
Jun 25, 2005·Journal of Medicinal Chemistry·Xavier Barril, S David Morley
Jul 28, 2005·Journal of Chemical Information and Modeling·Chidochangu P MpamhangaMika K Lindvall
Jul 28, 2005·Journal of Chemical Information and Modeling·Jinn-Moon YangD Frank Hsu
Jan 24, 2006·Journal of Chemical Information and Modeling·Philip Prathipati, Anil K Saxena
Jan 24, 2006·Journal of Chemical Information and Modeling·J Christian BaberMiklos Feher
Mar 14, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hossam M Ashtawy, Nihar R Mahapatra
Dec 1, 2004·Drug Discovery Today. Technologies·Tanja Schulz-Gasch, Martin Stahl

❮ Previous
Next ❯

Citations

Apr 20, 2010·Journal of Computer-aided Molecular Design·Natasja Brooijmans, Christine Humblet
May 3, 2011·Journal of Chemical Information and Modeling·Andreas SpitzmüllerGerhard Klebe
Jul 4, 2012·Journal of Chemical Information and Modeling·Daniel N SantiagoWesley H Brooks
Apr 16, 2013·Journal of Chemical Information and Modeling·Faisal SaeedAmmar Abdo
Jun 21, 2013·Journal of Chemical Information and Modeling·G Madhavi SastryWoody Sherman
Jan 10, 2013·Journal of Chemical Information and Modeling·Peter Willett
Mar 28, 2013·Journal of Chemical Information and Modeling·Khaled M Elokely, Robert J Doerksen
Oct 23, 2009·Journal of Chemical Information and Modeling·Hao FanAndrej Sali
Jul 25, 2012·Journal of Medicinal Chemistry·C David AnderssonAnna Linusson
Sep 13, 2008·Journal of Medicinal Chemistry·Pietro CozziniChristoph A Sotriffer
Dec 10, 2008·Chemical Research in Toxicology·Alessio AmadasiPietro Cozzini
Oct 3, 2009·Journal of Biomolecular Structure & Dynamics·Calvin Yu-Chian Chen
Dec 19, 2012·Journal of Cheminformatics·Faisal SaeedAmmar Abdo
Jan 16, 2013·Journal of Cheminformatics·Abhik SealDavid J Wild
Nov 26, 2013·Bioorganic Chemistry·Cevher Gundogdu-HizliatesLevent Cavas
Apr 1, 2009·Future Medicinal Chemistry·Age Aleksander SkjevikAurora Martinez
Apr 2, 2011·Future Medicinal Chemistry·John B O Mitchell
May 7, 2014·Journal of Chemical Information and Modeling·Marcelino Arciniega, Oliver F Lange
Nov 13, 2013·Future Medicinal Chemistry·Fernando V MalufRafael Vc Guido
Jul 25, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Leonardo G FerreiraAdriano D Andricopulo
Dec 31, 2010·Journal of Enzyme Inhibition and Medicinal Chemistry·Ghassan Abu SheikhaMutasem O Taha
Dec 28, 2010·Bioorganic Chemistry·Jiang WuY George Zheng
Aug 6, 2010·Drug Discovery Today·Stéphanie PérotBruno O Villoutreix
Jun 29, 2010·Journal of Molecular Graphics & Modelling·Jianxin DuanWoody Sherman
Aug 4, 2011·Journal of Chemical Information and Modeling·Richard D SmithHeather A Carlson
Jun 11, 2009·Drug Discovery Today·Markus H J Seifert
Feb 12, 2008·Biochemical and Biophysical Research Communications·Minyong LiBinghe Wang
Mar 18, 2008·Drug Discovery Today·Bohdan Waszkowycz
Nov 20, 2015·Journal of Chemical Information and Modeling·Woong-Hee ShinChaok Seok
Oct 17, 2007·Chemical Biology & Drug Design·Osman A B S M Gani
Nov 27, 2007·British Journal of Pharmacology·P TaylorM D Walkinshaw
Oct 21, 2010·Chemical Biology & Drug Design·Natasja Brooijmans, Christine Humblet
Feb 1, 2013·Molecular Informatics·Faisal SaeedHamza Hentabli
Jul 12, 2010·Molecular Informatics·Beining ChenPeter Willett
Apr 29, 2015·European Journal of Medicinal Chemistry·Teresa KasererDaniela Schuster
Jun 3, 2014·Journal of Cheminformatics·Ali AhmedAmmar Abdo
Apr 10, 2012·Bioorganic & Medicinal Chemistry·Chia-Wei ChuPeter Willett
Jan 24, 2009·Current Opinion in Structural Biology·Olgun Guvench, Alexander D MacKerell

❮ 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.