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From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side\u2010chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side\u2010chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side\u2010chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. \u00a9 1994 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.340190308","type":"journal-article","created":{"date-parts":[[2005,5,29]],"date-time":"2005-05-29T01:35:15Z","timestamp":1117330515000},"page":"244-255","source":"Crossref","is-referenced-by-count":38,"title":["Energy minimization method using automata network for sequence and side\u2010chain conformation prediction from given backbone geometry"],"prefix":"10.1002","volume":"19","author":[{"given":"Hidetoshi","family":"Kono","sequence":"first","affiliation":[]},{"given":"Junta","family":"Doi","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,2,3]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.2464850"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/0968-0004(89)90070-4"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.2392678"},{"key":"e_1_2_1_5_2","unstructured":"Sander C. ed. \u201cProtein Design Exercises 86.\u201d EMBL BIO\u2010computing Technical Document 1 1987."},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/3.4.259"},{"key":"e_1_2_1_7_2","first-page":"233","article-title":"The de novo design and the synthesis of \u03b1\/\u03b2\u2010barrel protein","volume":"14","author":"Tanaka T.","year":"1990","journal-title":"J. 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