{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T01:53:20Z","timestamp":1769133200482,"version":"3.49.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The increasing amount of data on protein\u2013protein interaction needs to be rationalized for deriving guidelines for the alteration or design of an interface between two proteins.<\/jats:p><jats:p>Results: We present a detaild structural analysis and comparison of homo- versus heterodimeric protein\u2013protein interfaces. Regular secondary structures (helices and strands) are the main components of the former, whereas non-regular structures (turns, loops, etc.) frequently mediate interactions in the latter. Interface helices get longer with increasing interface area, but only in heterocomplexes. On average, the homodimers have longer helical segments and prominent helix\u2013helix pairs. There is a surprising distinction in the relative orientation of interface helices, with a tendency for aligned packing in homodimers and a clear preference for packing at 90\u00b0 in heterodimers. Arg and the aromatic residues have a higher preference to occur in all secondary structural elements (SSEs) in the interface. Based on the dominant SSE, the interfaces have been grouped into four classes: \u03b1, \u03b2, \u03b1\u03b2 and non-regular. Identity between protein and interface classes is the maximum for \u03b1 proteins, but rather mediocre for the other protein classes. The interface classes of the two chains forming a heterodimer are often dissimilar. Eleven binding motifs can capture the prominent architectural features of most of the interfaces.<\/jats:p><jats:p>Contact: \u00a0pinak@boseinst.ernet.in<\/jats:p><jats:p>Supplementary information: A separate file is provided with 3 tables and 2 figures, which are referred to with a prefix \u2018S\u2019 in text.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm274","type":"journal-article","created":{"date-parts":[[2007,5,18]],"date-time":"2007-05-18T16:49:30Z","timestamp":1179506970000},"page":"1909-1918","source":"Crossref","is-referenced-by-count":155,"title":["Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein\u2013protein interactions"],"prefix":"10.1093","volume":"23","author":[{"given":"Mainak","family":"Guharoy","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Bose Institute, P-1\/12 CIT Scheme VIIM, Kolkata 700054, India"}]},{"given":"Pinak","family":"Chakrabarti","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Bose Institute, P-1\/12 CIT Scheme VIIM, Kolkata 700054, India"}]}],"member":"286","published-online":{"date-parts":[[2007,5,17]]},"reference":[{"key":"2023041105313049600_","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1093\/bioinformatics\/19.1.161","article-title":"InterPreTS: protein interaction prediction through tertiary structure","volume":"19","author":"Aloy","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041105313049600_","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1038\/nbt1018","article-title":"Ten thousand interactions for the molecular biologist","volume":"22","author":"Aloy","year":"2004","journal-title":"Nat. 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