Show simple item record

dc.contributor.authorSturm, Noe
dc.contributor.authorRognan, Didier
dc.contributor.authorQuinn, Ronald J
dc.contributor.authorKellenberger, Esther
dc.date.accessioned2017-11-28T04:12:47Z
dc.date.available2017-11-28T04:12:47Z
dc.date.issued2016
dc.identifier.issn1756-8919
dc.identifier.doi10.4155/fmc-2016-0077
dc.identifier.urihttp://hdl.handle.net/10072/100568
dc.description.abstractAim: We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction. Results: We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding. Conclusion: SiteAlign suits the comparison of binding sites for close or distant homologs. SiteAlign2 provides a better insight into the physical model of site similarity between nonhomologs, but at the expense of an increased sensitivity to atomic coordinates.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherFuture Science
dc.relation.ispartofpagefrom1871
dc.relation.ispartofpageto1885
dc.relation.ispartofissue15
dc.relation.ispartofjournalFuture Medicinal Chemistry
dc.relation.ispartofvolume8
dc.subject.fieldofresearchMedicinal and Biomolecular Chemistry not elsewhere classified
dc.subject.fieldofresearchMedicinal and Biomolecular Chemistry
dc.subject.fieldofresearchPharmacology and Pharmaceutical Sciences
dc.subject.fieldofresearchcode030499
dc.subject.fieldofresearchcode0304
dc.subject.fieldofresearchcode1115
dc.titleComparing atom-based with residue based descriptors in predicting binding site similarity: do backbone atoms matter?
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.facultyGriffith Sciences, Griffith Institute for Drug Discovery
gro.hasfulltextNo Full Text
gro.griffith.authorQuinn, Ronald J.
gro.griffith.authorSturm, Noe


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

  • Journal articles
    Contains articles published by Griffith authors in scholarly journals.

Show simple item record