Publication: Non-redundant unique interface structures as templates for modeling protein interactions
dc.contributor.coauthor | Nussinov, Ruth | |
dc.contributor.department | Department of Computer Engineering | |
dc.contributor.department | Graduate School of Sciences and Engineering | |
dc.contributor.department | Department of Chemical and Biological Engineering | |
dc.contributor.department | CCBB (The Center for Computational Biology and Bioinformatics) | |
dc.contributor.kuauthor | Gürsoy, Attila | |
dc.contributor.kuauthor | Çukuroğlu, Engin | |
dc.contributor.kuauthor | Keskin, Özlem | |
dc.contributor.kuprofile | Faculty Member | |
dc.contributor.kuprofile | PhD Student | |
dc.contributor.schoolcollegeinstitute | College of Engineering | |
dc.contributor.schoolcollegeinstitute | Graduate School of Sciences and Engineering | |
dc.contributor.schoolcollegeinstitute | Research Center | |
dc.contributor.yokid | 8745 | |
dc.contributor.yokid | N/A | |
dc.contributor.yokid | 26605 | |
dc.date.accessioned | 2024-11-09T12:17:24Z | |
dc.date.issued | 2014 | |
dc.description.abstract | Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions. Classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are 22604 unique interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at https://prism.ccbb.ku.edu.tr/piface. | |
dc.description.fulltext | YES | |
dc.description.indexedby | WoS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.issue | 1 | |
dc.description.openaccess | YES | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | N/A | |
dc.description.sponsorship | National Cancer Institute, National Institutes of Health | |
dc.description.sponsorship | NIH, National Cancer Institute, Center for Cancer Research | |
dc.description.version | Publisher version | |
dc.description.volume | 9 | |
dc.format | ||
dc.identifier.doi | 10.1371/journal.pone.0086738 | |
dc.identifier.eissn | 1932-6203 | |
dc.identifier.embargo | NO | |
dc.identifier.filenameinventoryno | IR00176 | |
dc.identifier.issn | 1932-6203 | |
dc.identifier.link | https://doi.org/10.1371/journal.pone.0086738 | |
dc.identifier.quartile | Q2 | |
dc.identifier.scopus | 2-s2.0-84900297215 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/1422 | |
dc.identifier.wos | 330507300105 | |
dc.keywords | Hot-spots | |
dc.keywords | Data-bank | |
dc.keywords | Homologous proteins | |
dc.keywords | Binding-energy | |
dc.keywords | Classification | |
dc.keywords | Complexes | |
dc.keywords | Sequence | |
dc.keywords | Database | |
dc.keywords | Motifs | |
dc.keywords | Similarities | |
dc.language | English | |
dc.publisher | Public Library of Science | |
dc.relation.grantno | HHSN261200800001E | |
dc.relation.uri | http://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/1205 | |
dc.source | PLOS One | |
dc.subject | Multidisciplinary sciences | |
dc.subject | Science and technology | |
dc.title | Non-redundant unique interface structures as templates for modeling protein interactions | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.authorid | 0000-0002-2297-2113 | |
local.contributor.authorid | N/A | |
local.contributor.authorid | 0000-0002-4202-4049 | |
local.contributor.kuauthor | Gürsoy, Attila | |
local.contributor.kuauthor | Çukuroğlu, Engin | |
local.contributor.kuauthor | Keskin, Özlem | |
local.publication.orgunit1 | College of Engineering | |
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