Determining protein similarity by comparing hydrophobic core structure

2017
journal article
article
6
cris.lastimport.wos2024-04-10T02:00:06Z
dc.abstract.enFormal assessment of structural similarity is − next to protein structure prediction − arguably the most important unsolved problem in proteomics. In this paper we propose a similarity criterion based on commonalities between the proteins’ hydrophobic cores. The hydrophobic core emerges as a result of conformational changes through which each residue reaches its intended position in the protein body. A quantitative criterion based on this phenomenon has been proposed in the framework of the CASP challenge. The structure of the hydrophobic core − including the placement and scope of any deviations from the idealized model − may indirectly point to areas of importance from the point of view of the protein’s biological function. Our analysis focuses on an arbitrarily selected target from the CASP11 challenge. The proposed measure, while compliant with CASP criteria (70–80% correlation), involves certain adjustments which acknowledge the presence of factors other than simple spatial arrangement of solids.pl
dc.affiliationWydział Lekarski : Zakład Bioinformatyki i Telemedycynypl
dc.affiliationWydział Fizyki, Astronomii i Informatyki Stosowanej : Zakład Technologii Informatycznychpl
dc.cm.id81886
dc.contributor.authorGadzała, M.pl
dc.contributor.authorKalinowska, Barbara - 114621 pl
dc.contributor.authorBanach, Mateusz - 103003 pl
dc.contributor.authorKonieczny, Leszekpl
dc.contributor.authorRoterman-Konieczna, Irena - 133298 pl
dc.date.accessioned2017-07-06T09:28:50Z
dc.date.available2017-07-06T09:28:50Z
dc.date.issued2017pl
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number2pl
dc.description.points15pl
dc.description.publication3,84pl
dc.description.versionostateczna wersja wydawcy
dc.description.volume3pl
dc.identifier.articleide00235pl
dc.identifier.doi10.1016/j.heliyon.2017.e00235pl
dc.identifier.eissn2405-8440pl
dc.identifier.projectROD UJ / Ppl
dc.identifier.urihttp://ruj.uj.edu.pl/xmlui/handle/item/42433
dc.languageengpl
dc.language.containerengpl
dc.rightsUdzielam licencji. Uznanie autorstwa - Użycie niekomercyjne - Bez utworów zależnych 4.0 Międzynarodowa*
dc.rights.licenceCC-BY-NC-ND
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.pl*
dc.scopuswos.indexingtakpl
dc.share.typeotwarte czasopismo
dc.subject.enbiological sciencespl
dc.subject.enbioinformaticspl
dc.subtypeArticlepl
dc.titleDetermining protein similarity by comparing hydrophobic core structurepl
dc.title.journalHeliyonpl
dc.typeJournalArticlepl
dspace.entity.typePublication
cris.lastimport.wos
2024-04-10T02:00:06Z
dc.abstract.enpl
Formal assessment of structural similarity is − next to protein structure prediction − arguably the most important unsolved problem in proteomics. In this paper we propose a similarity criterion based on commonalities between the proteins’ hydrophobic cores. The hydrophobic core emerges as a result of conformational changes through which each residue reaches its intended position in the protein body. A quantitative criterion based on this phenomenon has been proposed in the framework of the CASP challenge. The structure of the hydrophobic core − including the placement and scope of any deviations from the idealized model − may indirectly point to areas of importance from the point of view of the protein’s biological function. Our analysis focuses on an arbitrarily selected target from the CASP11 challenge. The proposed measure, while compliant with CASP criteria (70–80% correlation), involves certain adjustments which acknowledge the presence of factors other than simple spatial arrangement of solids.
dc.affiliationpl
Wydział Lekarski : Zakład Bioinformatyki i Telemedycyny
dc.affiliationpl
Wydział Fizyki, Astronomii i Informatyki Stosowanej : Zakład Technologii Informatycznych
dc.cm.id
81886
dc.contributor.authorpl
Gadzała, M.
dc.contributor.authorpl
Kalinowska, Barbara - 114621
dc.contributor.authorpl
Banach, Mateusz - 103003
dc.contributor.authorpl
Konieczny, Leszek
dc.contributor.authorpl
Roterman-Konieczna, Irena - 133298
dc.date.accessioned
2017-07-06T09:28:50Z
dc.date.available
2017-07-06T09:28:50Z
dc.date.issuedpl
2017
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.numberpl
2
dc.description.pointspl
15
dc.description.publicationpl
3,84
dc.description.version
ostateczna wersja wydawcy
dc.description.volumepl
3
dc.identifier.articleidpl
e00235
dc.identifier.doipl
10.1016/j.heliyon.2017.e00235
dc.identifier.eissnpl
2405-8440
dc.identifier.projectpl
ROD UJ / P
dc.identifier.uri
http://ruj.uj.edu.pl/xmlui/handle/item/42433
dc.languagepl
eng
dc.language.containerpl
eng
dc.rights*
Udzielam licencji. Uznanie autorstwa - Użycie niekomercyjne - Bez utworów zależnych 4.0 Międzynarodowa
dc.rights.licence
CC-BY-NC-ND
dc.rights.uri*
http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.pl
dc.scopuswos.indexingpl
tak
dc.share.type
otwarte czasopismo
dc.subject.enpl
biological sciences
dc.subject.enpl
bioinformatics
dc.subtypepl
Article
dc.titlepl
Determining protein similarity by comparing hydrophobic core structure
dc.title.journalpl
Heliyon
dc.typepl
JournalArticle
dspace.entity.type
Publication
Affiliations

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