Ten quick tips for homology modeling of high-resolution protein 3D structures

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dc.contributor.authorHaddad, Yazan Abdulmajeed Eyadhcs
dc.contributor.authorAdam, Vojtěchcs
dc.contributor.authorHeger, Zbyněkcs
dc.coverage.issue4cs
dc.coverage.volume16cs
dc.date.accessioned2020-08-04T11:58:01Z
dc.date.available2020-08-04T11:58:01Z
dc.date.issued2020-04-30cs
dc.description.abstractThe purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.en
dc.formattextcs
dc.format.extent1-19cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationPLoS Computational Biology. 2020, vol. 16, issue 4, p. 1-19.en
dc.identifier.doi10.1371/journal.pcbi.1007449cs
dc.identifier.issn1553-734Xcs
dc.identifier.other164134cs
dc.identifier.urihttp://hdl.handle.net/11012/188175
dc.language.isoencs
dc.publisherPLOScs
dc.relation"European Union (EU)" & "Horizon 2020"
dc.relation.ispartofPLoS Computational Biologycs
dc.relation.projectIdinfo:eu-repo/grantAgreement/EC/H2020/759585/EU//ToMeTuM
dc.relation.urihttps://doi.org/10.1371/journal.pcbi.1007449cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1553-734X/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectprotein 3D structuresen
dc.subjectrepositoriesen
dc.subjecthomology modelingen
dc.subjectmolecular docking and molecular dynamicsen
dc.titleTen quick tips for homology modeling of high-resolution protein 3D structuresen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-164134en
sync.item.dbtypeVAVen
sync.item.insts2020.08.04 13:58:01en
sync.item.modts2020.08.04 12:50:59en
thesis.grantorVysoké učení technické v Brně. Středoevropský technologický institut VUT. Chytré nanonástrojecs
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