Publication:
Prism: protein-protein interaction prediction by structural matching

dc.contributor.coauthorNussinov, Ruth
dc.contributor.departmentDepartment of Computer Engineering
dc.contributor.departmentDepartment of Chemical and Biological Engineering
dc.contributor.departmentCCBB (The Center for Computational Biology and Bioinformatics)
dc.contributor.kuauthorGürsoy, Attila
dc.contributor.kuauthorKeskin, Özlem
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteResearch Center
dc.date.accessioned2024-11-09T23:01:34Z
dc.date.issued2008
dc.description.abstractPrism (protein interactions by structural matching) is a system that employs a novel prediction algorithm for protein-protein interactions. It adopts a bottom-up approach that combines structure and sequence conservation in protein interfaces. The algorithm seeks possible binary interactions between proteins through structure similarity and evolutionary conservation of known interfaces. It is composed of a database containing protein interface Structures derived from the Protein Data Bank (PDB) and predicted protein-protein interactions. It also provides related information about the proteins and in interactive protein interface viewer. In the current version, 3799 structurally nonredundant interfaces tire used to predict the interactions among 6170 proteins. A substantial number of interactions are verified in two publicly available interaction databases (DIP and BIND). As the verified interactions demonstrate the Suitability of our approach, unverified ones may point to undiscovered interactions. Prism can be accessed through a user-friendly website (http://prism.ccbb.ku.edu.tr) and it will be updated regularly as new protein structures become available in the PDB. Users may browse through the nonredundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of structures similar to these interfaces, or see the results of interaction predictions for a particular protein. Another service provided is the interactive prediction. This is done by running the algorithm for the user input structures.
dc.description.indexedbyWOS
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuN/A
dc.description.sponsorshipIntramural NIH HHS [Z01 BC010441-06] Funding Source: Medline
dc.description.sponsorshipNCI NIH HHS [N01CO12400, N01-CO-12400] Funding Source: Medline
dc.description.volume484
dc.identifier.doi10.1007/978-1-59745-398-1
dc.identifier.eissn1940-6029
dc.identifier.isbn978-1-58829-971-0
dc.identifier.issn1064-3745
dc.identifier.scopus2-s2.0-60349125228
dc.identifier.urihttps://hdl.handle.net/20.500.14288/8259
dc.identifier.wos268729100030
dc.keywordsProtein interactions
dc.keywordsProtein interaction prediction
dc.keywordsProtein interfaces
dc.keywordsProtein databases
dc.keywordsHot-spots
dc.keywordsInteraction sites
dc.keywordsOrganization
dc.keywordsInterfaces
dc.keywordsDatabase
dc.language.isoeng
dc.publisherHumana Press inc
dc.relation.ispartofFunctional Proteomics: Methods and Protocols
dc.subjectBiochemical research methods
dc.titlePrism: protein-protein interaction prediction by structural matching
dc.typeBook Chapter
dspace.entity.typePublication
local.contributor.kuauthorKeskin, Özlem
local.contributor.kuauthorGürsoy, Attila
local.publication.orgunit1College of Engineering
local.publication.orgunit1Research Center
local.publication.orgunit2Department of Chemical and Biological Engineering
local.publication.orgunit2Department of Computer Engineering
local.publication.orgunit2CCBB (The Center for Computational Biology and Bioinformatics)
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