{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T23:18:40Z","timestamp":1776122320945,"version":"3.50.1"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>In peptides and proteins, only a small percentile of peptide bonds adopts the <jats:italic>cis<\/jats:italic> configuration. Especially in the case of amide peptide bonds, the amount of <jats:italic>cis<\/jats:italic> conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline <jats:italic>cis<\/jats:italic> formations (<jats:italic>cis<\/jats:italic>-nonPro).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the <jats:italic>cis<\/jats:italic>-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with <jats:italic>cis<\/jats:italic>-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between <jats:italic>cis<\/jats:italic>-nonPro and <jats:italic>trans<\/jats:italic>-nonPro formations.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>In terms of functional implications, we observe a significant association of <jats:italic>cis<\/jats:italic>-nonPro peptide bonds towards ligand\/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-142","type":"journal-article","created":{"date-parts":[[2011,5,11]],"date-time":"2011-05-11T06:27:02Z","timestamp":1305095222000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment"],"prefix":"10.1186","volume":"12","author":[{"given":"Konstantinos P","family":"Exarchos","sequence":"first","affiliation":[]},{"given":"Themis P","family":"Exarchos","sequence":"additional","affiliation":[]},{"given":"Georgios","family":"Rigas","sequence":"additional","affiliation":[]},{"given":"Costas","family":"Papaloukas","sequence":"additional","affiliation":[]},{"given":"Dimitrios I","family":"Fotiadis","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,5,10]]},"reference":[{"key":"4483_CR1","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/1368","volume":"5","author":"MS Weiss","year":"1998","unstructured":"Weiss MS, Jabs A, Hilgenfeld R: Peptide bonds revisited. 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