NDLI: Molecular dynamics to enhance structure-based virtual screening on cathepsin B

Content Provider	Springer Nature Link
Author	Ogrizek, Mitja Turk, Samo Lešnik, Samo Sosič, Izidor Hodošček, Milan Mirković, Bojana Kos, Janko Janežič, Dušanka Gobec, Stanislav Konc, Janez
Copyright Year	2015
Abstract	Molecular dynamics (MD) and molecular docking are commonly used to study molecular interactions in drug discovery. Most docking approaches consider proteins as rigid, which can decrease the accuracy of predicted docked poses. Therefore MD simulations can be used prior to docking to add flexibility to proteins. We evaluated the contribution of using MD together with docking in a docking study on human cathepsin B, a well-studied protein involved in numerous pathological processes. Using CHARMM biomolecular simulation program and AutoDock Vina molecular docking program, we found, that short MD simulations significantly improved molecular docking. Our results, expressed with the area under the receiver operating characteristic curves, show an increase in discriminatory power i.e. the ability to discriminate active from inactive compounds of molecular docking, when docking is performed to selected snapshots from MD simulations.
Starting Page	707
Ending Page	712
Page Count	6
File Format	PDF
ISSN	0920654X
Journal	Journal of Computer-Aided Molecular Design
Volume Number	29
Issue Number	8
e-ISSN	15734951
Language	English
Publisher	Springer International Publishing
Publisher Date	2015-05-07
Publisher Place	Cham
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Cathepsin B Molecular dynamics Molecular docking Protein flexibility Physical Chemistry Computer Applications in Chemistry Animal Anatomy / Morphology / Histology
Content Type	Text
Resource Type	Article
Subject	Drug Discovery Physical and Theoretical Chemistry Computer Science Applications

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