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A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

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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.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorGürsoy, Attila
dc.contributor.kuauthorKeskin, Özlem
dc.contributor.kuauthorMakinacı, Gözde Kar
dc.contributor.kuauthorTunçbağ, Nurcan
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.contributor.schoolcollegeinstituteResearch Center
dc.date.accessioned2024-11-09T23:13:29Z
dc.date.issued2009
dc.description.abstractThe unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue3
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuN/A
dc.description.sponsorshipTurkish Academy of Sciences Distinguished Young Investigator Award
dc.description.sponsorshipScientific and Technological Research Council of Turkey
dc.description.sponsorshipNational Cancer Institute
dc.description.sponsorshipNational Institutes of Health [N01-CO-12400]
dc.description.sponsorshipCenter for Cancer Research (partial) Turkish Academy of Sciences Distinguished Young Investigator Award (to O.K.)
dc.description.sponsorshipthe Scientific and Technological Research Council of Turkey Fellowship (to N.T.). Federal funds from the National Cancer Institute
dc.description.sponsorshipNational Institutes of Health
dc.description.sponsorship(under contract number N01-CO-12400). Intramural Research Program of the National Institutes of Health
dc.description.sponsorshipNational Cancer Institute
dc.description.sponsorshipCenter for Cancer Research (partial).
dc.description.volume10
dc.identifier.doi10.1093/bib/bbp001
dc.identifier.eissn1477-4054
dc.identifier.issn1467-5463
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-65549157572
dc.identifier.urihttps://doi.org/10.1093/bib/bbp001
dc.identifier.urihttps://hdl.handle.net/20.500.14288/9980
dc.identifier.wos265522200002
dc.keywordsProtein-protein interactions
dc.keywordsProtein-protein interfaces
dc.keywordsBinding site prediction
dc.keywordsDocking
dc.keywordsWeb servers
dc.keywordsDatabases
dc.keywordsBinding site prediction
dc.keywordsHot-spots
dc.keywordsShape complementarity
dc.keywordsQuaternary structure
dc.keywordsDomain-domain
dc.keywordsDatabase
dc.keywordsResidues
dc.keywordsConservation
dc.keywordsRecognition
dc.keywordsComplexes
dc.language.isoeng
dc.publisherOxford University Press (OUP)
dc.relation.ispartofBriefings in Bioinformatics
dc.subjectBiochemical research methods
dc.subjectMathematical and computational biology
dc.titleA survey of available tools and web servers for analysis of protein-protein interactions and interfaces
dc.typeReview
dspace.entity.typePublication
local.contributor.kuauthorKeskin, Özlem
local.contributor.kuauthorGürsoy, Attila
local.contributor.kuauthorMakinacı, Gözde Kar
local.contributor.kuauthorTunçbağ, Nurcan
local.publication.orgunit1College of Engineering
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND 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)
local.publication.orgunit2Graduate School of Sciences and Engineering
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