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Molecular dynamics to enhance structure-based virtual screening on cathepsin BOgrizek, Mitja ...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 adocking 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 selectedsnapshots from MD simulations.Source: Journal of computer-aided molecular design. - ISSN 0920-654X (Vol. 29, iss. 8, 2015, str. 707-712)Type of material - article, component partPublish date - 2015Language - englishCOBISS.SI-ID - 3858033
Author
Ogrizek, Mitja |
Turk, Samo, farmacevt |
Lešnik, Samo |
Sosič, Izidor |
Hodošček, Milan |
Mirković, Bojana |
Kos, Janko, 1959- |
Janežič, Dušanka, 1952- |
Gobec, Stanislav, 1970- |
Konc, Janez
Topics
katepsin B |
molekularna dinamika |
molekularno krajšanje |
proteinska prožnost |
raziskava zdravil
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source: Journal of computer-aided molecular design. - ISSN 0920-654X (Vol. 29, iss. 8, 2015, str. 707-712)
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Database name | Field | Year |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Ogrizek, Mitja | 34598 |
Turk, Samo, farmacevt | 29773 |
Lešnik, Samo | 37452 |
Sosič, Izidor | 30816 |
Hodošček, Milan | 02287 |
Mirković, Bojana | 29604 |
Kos, Janko, 1959- | 04648 |
Janežič, Dušanka, 1952- | 06734 |
Gobec, Stanislav, 1970- | 15284 |
Konc, Janez | 25435 |
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