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Article: How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

TitleHow well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases
Authors
Issue Date2012
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/srep/index.html
Citation
Scientific Reports, 2012, v. 2, article no. 323 How to Cite?
AbstractMolecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by independent scientists comparing the performance of the docking programs by using default 'black boxg' protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the 'Key Interaction Score Systemg' (KISS), a more biochemically meaningful measure for evaluation of docking programs based on pose prediction accuracy.
Persistent Identifierhttp://hdl.handle.net/10722/181264
ISSN
2015 Impact Factor: 5.228
2015 SCImago Journal Rankings: 2.073
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorUdatha, DBRKGen_US
dc.contributor.authorSugaya, Nen_US
dc.contributor.authorOlsson, Len_US
dc.contributor.authorPanagiotou, Gen_US
dc.date.accessioned2013-02-21T02:03:36Z-
dc.date.available2013-02-21T02:03:36Z-
dc.date.issued2012en_US
dc.identifier.citationScientific Reports, 2012, v. 2, article no. 323en_US
dc.identifier.issn2045-2322en_US
dc.identifier.urihttp://hdl.handle.net/10722/181264-
dc.description.abstractMolecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by independent scientists comparing the performance of the docking programs by using default 'black boxg' protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the 'Key Interaction Score Systemg' (KISS), a more biochemically meaningful measure for evaluation of docking programs based on pose prediction accuracy.en_US
dc.languageengen_US
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/srep/index.htmlen_US
dc.relation.ispartofScientific Reportsen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleHow well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterasesen_US
dc.typeArticleen_US
dc.identifier.emailPanagiotou, G: gipa@hku.hken_US
dc.identifier.authorityPanagiotou, G=rp01725en_US
dc.description.naturepublished_or_final_versionen_US
dc.identifier.doi10.1038/srep00323en_US
dc.identifier.pmid22435086-
dc.identifier.scopuseid_2-s2.0-84859746204en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84859746204&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume2en_US
dc.identifier.spagearticle no. 323-
dc.identifier.spagearticle no. 323-
dc.identifier.isiWOS:000301775600002-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridUdatha, DBRKG=36704182100en_US
dc.identifier.scopusauthoridSugaya, N=55185419500en_US
dc.identifier.scopusauthoridOlsson, L=7203077540en_US
dc.identifier.scopusauthoridPanagiotou, G=8566179700en_US

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