Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.

Acta Pharmacologica Sinica
Zhi ChenHua-liang Jiang

Abstract

This study was conducted to compare the efficiencies of two virtual screening approaches, pharmacophore-based virtual screening (PBVS) and docking-based virtual screening (DBVS) methods. All virtual screens were performed on two data sets of small molecules with both actives and decoys against eight structurally diverse protein targets, namely angiotensin converting enzyme (ACE), acetylcholinesterase (AChE), androgen receptor (AR), D-alanyl-D-alanine carboxypeptidase (DacA), dihydrofolate reductase (DHFR), estrogen receptors alpha (ERalpha), HIV-1 protease (HIV-pr), and thymidine kinase (TK). Each pharmacophore model was constructed based on several X-ray structures of protein-ligand complexes. Virtual screens were performed using four screening standards, the program Catalyst for PBVS and three docking programs (DOCK, GOLD and Glide) for DBVS. Of the sixteen sets of virtual screens (one target versus two testing databases), the enrichment factors of fourteen cases using the PBVS method were higher than those using DBVS methods. The average hit rates over the eight targets at 2% and 5% of the highest ranks of the entire databases for PBVS are much higher than those for DBVS. The PBVS method outperformed DBVS methods in retrievi...Continue Reading

References

Jan 1, 1976·Annual Review of Biochemistry·R L Soffer
Jan 27, 1995·Journal of Molecular Biology·D H JonesA Aitken
Mar 14, 1997·Journal of Medicinal Chemistry·K BäckbroA Hallberg
Apr 4, 1997·Journal of Molecular Biology·G JonesR Taylor
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 2, 2000·Journal of Computer-aided Molecular Design·U Norinder
Jun 8, 2001·Journal of Computer-aided Molecular Design·T J EwingI D Kuntz
Jul 27, 2001·Current Medicinal Chemistry·Y Kurogi, O F Güner
Mar 5, 2002·Molecular Endocrinology·Elin HolterEckardt Treuter
Mar 22, 2002·Journal of Medicinal Chemistry·Albert PalomerAntonio Espinosa
May 17, 2002·Journal of Medicinal Chemistry·Thompson N DomanBrian K Shoichet
Oct 29, 2002·Proteins·J Willem M NissinkRobin Taylor
Aug 12, 2003·Proteins·Marcel L VerdonkRichard D Taylor
Oct 8, 2003·Current Medicinal Chemistry·Jianhua ShenHualiang Jiang
Mar 19, 2004·Journal of Medicinal Chemistry·Richard A FriesnerPeter S Shenkin
Apr 10, 2004·Journal of Computer-aided Molecular Design·Badry D BursulayaCharles L Brooks
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·Jason R SchnellPeter E Wright
Dec 17, 2004·Nature·Brian K Shoichet
Jan 26, 2005·Journal of Chemical Information and Modeling·Eva M KrovatThierry Langer
Jan 26, 2005·Journal of Chemical Information and Modeling·Gerhard Wolber, Thierry Langer
Feb 18, 2005·Journal of Medicinal Chemistry·Maxwell D CummingsEdward P Jaeger
Dec 31, 2005·Nucleic Acids Research·David S WishartJennifer Woolsey
Jan 24, 2006·Journal of Chemical Information and Modeling·Hongming ChenJin Li
May 12, 2006·Journal of Medicinal Chemistry·Ann E Cleves, Ajay N Jain
Sep 29, 2006·Journal of Medicinal Chemistry·Gregory L WarrenMartha S Head
Oct 16, 2007·Current Opinion in Chemical Biology·Campbell McInnes

❮ Previous
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Citations

Sep 29, 2011·International Journal of Molecular Sciences·Chia-Hsien LeeHsueh-Fen Juan
Jun 26, 2015·International Journal of Molecular Sciences·Nannan ZhouHualiang Jiang
Sep 27, 2015·Journal of Computer-aided Molecular Design·Sanna P NiinivehmasOlli T Pentikäinen
Apr 16, 2016·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Rachel A HodosJoel T Dudley
Jul 30, 2014·Journal of Molecular Graphics & Modelling·Sofiene LarifKamel Bouraoui
May 24, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yanyan ShaoLanzhen Zhang
Jan 11, 2017·Journal of Chemical Information and Modeling·Marcus WiederThierry Langer
Jun 8, 2017·Journal of Biomolecular Structure & Dynamics·Chandrasekaran RamakrishnanM Michael Gromiha
Jan 19, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bin LiYanjiang Qiao
Dec 29, 2017·Journal of Biomolecular Structure & Dynamics·Chirag N PatelHimanshu A Pandya
Aug 10, 2010·Molecular BioSystems·Alberto Del RioGiuseppe Felice Mangiatordi
Oct 3, 2019·Protein Science : a Publication of the Protein Society·Ji Young LeeIvet Bahar
Jun 6, 2018·Frontiers in Chemistry·Hongbin HuangZunnan Huang
Jan 31, 2019·International Journal of Molecular Sciences·Yunhui PengSankar Basu
May 14, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Valentina TortosaFabio Polticelli
Jun 20, 2019·Frontiers in Pharmacology·Rosalia PascualJosé Miguel Vela
Oct 10, 2020·Journal of Biomolecular Structure & Dynamics·Dhananjay D JadeDinesh Gupta
Oct 23, 2020·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Louis ThesnaarTheunis T Cloete
Apr 17, 2021·Bioorganic & Medicinal Chemistry·Nicole L RichardsonLuke Hunter
Jun 22, 2021·ACS Pharmacology & Translational Science·Kader SahinSerdar Durdagi
May 28, 2010·Journal of Chemical Information and Modeling·Salla I Virtanen, Olli T Pentikäinen
Jul 9, 2020·Journal of Chemical Information and Modeling·Siduo JiangDavid E Shaw
Jun 1, 2012·Journal of Chemical Information and Modeling·Marijn P A SandersAlberto Del Rio

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