Publication: Prism: protein-protein interaction prediction by structural matching
dc.contributor.coauthor | Nussinov, Ruth | |
dc.contributor.department | Department of Computer 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 | Keskin, Özlem | |
dc.contributor.schoolcollegeinstitute | College of Engineering | |
dc.contributor.schoolcollegeinstitute | Research Center | |
dc.date.accessioned | 2024-11-09T23:01:34Z | |
dc.date.issued | 2008 | |
dc.description.abstract | Prism (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.indexedby | WOS | |
dc.description.openaccess | YES | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | N/A | |
dc.description.sponsorship | Intramural NIH HHS [Z01 BC010441-06] Funding Source: Medline | |
dc.description.sponsorship | NCI NIH HHS [N01CO12400, N01-CO-12400] Funding Source: Medline | |
dc.description.volume | 484 | |
dc.identifier.doi | 10.1007/978-1-59745-398-1 | |
dc.identifier.eissn | 1940-6029 | |
dc.identifier.isbn | 978-1-58829-971-0 | |
dc.identifier.issn | 1064-3745 | |
dc.identifier.scopus | 2-s2.0-60349125228 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/8259 | |
dc.identifier.wos | 268729100030 | |
dc.keywords | Protein interactions | |
dc.keywords | Protein interaction prediction | |
dc.keywords | Protein interfaces | |
dc.keywords | Protein databases | |
dc.keywords | Hot-spots | |
dc.keywords | Interaction sites | |
dc.keywords | Organization | |
dc.keywords | Interfaces | |
dc.keywords | Database | |
dc.language.iso | eng | |
dc.publisher | Humana Press inc | |
dc.relation.ispartof | Functional Proteomics: Methods and Protocols | |
dc.subject | Biochemical research methods | |
dc.title | Prism: protein-protein interaction prediction by structural matching | |
dc.type | Book Chapter | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Keskin, Özlem | |
local.contributor.kuauthor | Gürsoy, Attila | |
local.publication.orgunit1 | College of Engineering | |
local.publication.orgunit1 | Research Center | |
local.publication.orgunit2 | Department of Chemical and Biological Engineering | |
local.publication.orgunit2 | Department of Computer Engineering | |
local.publication.orgunit2 | CCBB (The Center for Computational Biology and Bioinformatics) | |
relation.isOrgUnitOfPublication | 89352e43-bf09-4ef4-82f6-6f9d0174ebae | |
relation.isOrgUnitOfPublication | c747a256-6e0c-4969-b1bf-3b9f2f674289 | |
relation.isOrgUnitOfPublication | d31df7d7-274a-4cdd-9166-96a14ab5b0a0 | |
relation.isOrgUnitOfPublication.latestForDiscovery | 89352e43-bf09-4ef4-82f6-6f9d0174ebae | |
relation.isParentOrgUnitOfPublication | 8e756b23-2d4a-4ce8-b1b3-62c794a8c164 | |
relation.isParentOrgUnitOfPublication | d437580f-9309-4ecb-864a-4af58309d287 | |
relation.isParentOrgUnitOfPublication.latestForDiscovery | 8e756b23-2d4a-4ce8-b1b3-62c794a8c164 |