{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:48:56Z","timestamp":1773283736557,"version":"3.50.1"},"reference-count":13,"publisher":"SAGE Publications","issue":"3","license":[{"start":{"date-parts":[[2012,3,1]],"date-time":"2012-03-01T00:00:00Z","timestamp":1330560000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Journal of Computational Biology"],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    In this article, we address the problem of designing a string with optimal complementarity properties with respect to another given string according to a given criterion. The motivation comes from a drug design application, in which the complementarity between two sequences (proteins) is measured according to the values of the hydropathic coefficients associated with the sequence elements (amino acids). We present heuristic and exact optimization algorithms, and we report on some computational experiments on amino peptides taken from Semaphorin and human Interleukin-1\n                    <jats:italic toggle=\"yes\">\u03b2<\/jats:italic>\n                    , which have already been investigated in the literature using heuristic algorithms. With our techniques, we proved the optimality of a known solution for Semaphorin-3A, and we discovered several other optimal and near-optimal solutions in a short computing time; we also found in fractions of a second an optimal solution for human interleukin-1\n                    <jats:italic toggle=\"yes\">\u03b2<\/jats:italic>\n                    , whose complementary value is one order of magnitude better than previously known ones. The source code of a prototype C++ implementation of our algorithms is freely available for noncommercial use on the web. As a main result, we showed that in this context mathematical programming methods are more successful than heuristics, such as simulated annealing. Our algorithm unfolds its potential, especially when different measures could be used for scoring peptides, and is able to provide not only a single optimal solution, but a ranking of provable good ones; this ranking can then be used by biologists as a starting basis for further refinements, simulations, or\n                    <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                    experiments.\n                  <\/jats:p>","DOI":"10.1089\/cmb.2011.0084","type":"journal-article","created":{"date-parts":[[2012,3,8]],"date-time":"2012-03-08T12:43:21Z","timestamp":1331210601000},"page":"261-270","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Algorithms for the Design of Maximum Hydropathic Complementarity Molecules"],"prefix":"10.1177","volume":"19","author":[{"given":"Alberto","family":"Ceselli","sequence":"first","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano","place":["Italy"]}]},{"given":"Sandro Luciano","family":"Fornili","sequence":"additional","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano","place":["Italy"]}]},{"given":"Giovanni","family":"Righini","sequence":"additional","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano","place":["Italy"]}]}],"member":"179","published-online":{"date-parts":[[2012,3,8]]},"reference":[{"key":"e_1_3_2_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm0995-894"},{"key":"e_1_3_2_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm0995-876"},{"key":"e_1_3_2_4_1","unstructured":"Ceselli A. Fornili S. Righini G. 2010. HCM web page. www.dti.unimi.it\/ceselli\/HCM.html. 2011 November 1."},{"key":"e_1_3_2_5_1","first-page":"345","article-title":"A model of evolutionary change in proteins","volume":"5","author":"Dayhoff M.","year":"1978","unstructured":"Dayhoff M., , Schwartz R., , Orcutt B. 1978. A model of evolutionary change in proteins. Atlas Protein Seq. Struct., 5:345\u2013352.","journal-title":"Atlas Protein Seq. Struct."},{"key":"e_1_3_2_6_1","doi-asserted-by":"publisher","DOI":"10.1042\/bj2820773"},{"key":"e_1_3_2_7_1","volume-title":"Computers and Intractability: A Guide to the Theory of NP-Completeness","author":"Garey M.","year":"1979","unstructured":"Garey M., , Johnson D. 1979. Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman: New York."},{"key":"e_1_3_2_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/1439-7633(20020301)3:2\/3<136::AID-CBIC136>3.0.CO;2-7"},{"key":"e_1_3_2_9_1","first-page":"245","article-title":"Evaluation of protein hydropathy scales","author":"J\u00e4\u00e4skel\u00e4inen S.","year":"2007","unstructured":"J\u00e4\u00e4skel\u00e4inen S., , Riikonen P., , Salakoski T. et al. 2007. Evaluation of protein hydropathy scales. Proc. IEEE Int. Conf. Bioinform. Biomed., 245\u2013251.","journal-title":"Proc. IEEE Int. Conf. Bioinform. Biomed."},{"key":"e_1_3_2_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90515-0"},{"key":"e_1_3_2_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-97"},{"key":"e_1_3_2_12_1","doi-asserted-by":"publisher","DOI":"10.1137\/0203021"},{"key":"e_1_3_2_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm1361"},{"key":"e_1_3_2_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1471-4159.2004.02950.x"}],"container-title":["Journal of Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/cmb.2011.0084","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/cmb.2011.0084","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/cmb.2011.0084","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T11:33:12Z","timestamp":1773228792000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1089\/cmb.2011.0084"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,1]]},"references-count":13,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2012,3,1]]}},"alternative-id":["10.1089\/cmb.2011.0084"],"URL":"https:\/\/doi.org\/10.1089\/cmb.2011.0084","relation":{},"ISSN":["1066-5277","1557-8666"],"issn-type":[{"value":"1066-5277","type":"print"},{"value":"1557-8666","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,3,1]]}}}