{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T06:40:40Z","timestamp":1771915240409,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Design of protein\u2013protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides, especially short ones (5\u201315 amino acid long), are natural candidates for inhibition of protein\u2013protein complexes due to several attractive features such as high structural compatibility with the protein binding site (mimicking the surface of one of the proteins), small size and the ability to form strong hotspot binding connections with the protein surface. Efficient rational peptide design is still a major challenge in computer aided drug design, due to the huge space of possible sequences, which is exponential in the length of the peptide, and the high flexibility of peptide conformations.<\/jats:p>\n               <jats:p>Results: In this article we present PinaColada, a novel computational method for the design of peptide inhibitors for protein\u2013protein interactions. We employ a version of the ant colony optimization heuristic, which is used to explore the exponential space (20n) of length n peptide sequences, in combination with our fast robotics motivated PepCrawler algorithm, which explores the conformational space for each candidate sequence. PinaColada is being run in parallel, on a DELL PowerEdge 2.8\u2009GHZ computer with 20 cores and 256\u2009GB memory, and takes up to 24\u2009h to design a peptide of 5-15 amino acids length.<\/jats:p>\n               <jats:p>Availability and implementation: An online server available at: http:\/\/bioinfo3d.cs.tau.ac.il\/PinaColada\/.<\/jats:p>\n               <jats:p>Contact: \u00a0danielza@post.tau.ac.il; wolfson@tau.ac.il<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw133","type":"journal-article","created":{"date-parts":[[2016,3,13]],"date-time":"2016-03-13T01:18:47Z","timestamp":1457831927000},"page":"2289-2296","source":"Crossref","is-referenced-by-count":30,"title":["PinaColada: peptide\u2013inhibitor ant colony ad-hoc design algorithm"],"prefix":"10.1093","volume":"32","author":[{"given":"Daniel","family":"Zaidman","sequence":"first","affiliation":[{"name":"Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel"}]},{"given":"Haim J.","family":"Wolfson","sequence":"additional","affiliation":[{"name":"Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel"}]}],"member":"286","published-online":{"date-parts":[[2016,3,11]]},"reference":[{"key":"2023020112471346900_btw133-B1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/prot.21495","article-title":"FireDock: Fast interaction refinement in molecular docking","volume":"69","author":"Andrusier","year":"2007","journal-title":"Proteins"},{"key":"2023020112471346900_btw133-B2","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/nrd1343","article-title":"Small-molecule inhibitors of protein\u2013protein interactions: progressing towards the dream","volume":"3","author":"Arkin","year":"2004","journal-title":"Nat. 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