{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T07:32:39Z","timestamp":1771486359947,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models.<\/jats:p><jats:p>Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.<\/jats:p><jats:p>Availability: The new term is implemented within the MESHI package and is freely available at http:\/\/cs.bgu.ac.il\/\u223cmeshi.<\/jats:p><jats:p>Contact: \u00a0chen.keasar@gmail.com<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp449","type":"journal-article","created":{"date-parts":[[2009,7,24]],"date-time":"2009-07-24T00:55:41Z","timestamp":1248396941000},"page":"2639-2645","source":"Crossref","is-referenced-by-count":35,"title":["Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential"],"prefix":"10.1093","volume":"25","author":[{"given":"Ami","family":"Levy-Moonshine","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"El-ad David","family":"Amir","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Keasar","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"},{"name":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,7,23]]},"reference":[{"key":"2023013112124215900_B1","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1002\/prot.21896","article-title":"Differentiabl,e multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities","volume":"72","author":"Amir","year":"2008","journal-title":"Proteins"},{"key":"2023013112124215900_B2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/0079-6107(84)90007-5","article-title":"Hydrogen bonding in globular proteins","volume":"44","author":"Backer","year":"1984","journal-title":"Prog. 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