{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T17:51:37Z","timestamp":1759341097677},"reference-count":19,"publisher":"World Scientific Pub Co Pte Lt","issue":"02","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2005,4]]},"abstract":"<jats:p> Self-organizing map (SOM) has been used in protein folding prediction when the HP model is employed. The existing work uses a square-like shape lattice with l = m\u00d7n points to represent the optimal compact structure of a sequence of l amino acids. In this paper, a general l\u2032-size sequence of amino acids is self-organized in a two dimensional lattice with l (&gt; l\u2032) points. The obtained minimum configuration then has a flexible shape, in contrast to the compact structure limited in the lattice. To fulfil this extension, a new self-organizing map (SOM) technique is proposed to deal with the difficulty of the unsymmetric input and output spaces. New competition rules in the training phase are introduced and a local search method is applied to overcome the multi-mapping phenomena. Several HP benchmark examples with up to 36 amino acids are tested to verify the effectiveness of the proposed approach in this paper. <\/jats:p>","DOI":"10.1142\/s0219720005001107","type":"journal-article","created":{"date-parts":[[2005,4,15]],"date-time":"2005-04-15T11:52:15Z","timestamp":1113565935000},"page":"385-400","source":"Crossref","is-referenced-by-count":13,"title":["EXPLORING PROTEIN'S OPTIMAL HP CONFIGURATIONS BY SELF-ORGANIZING MAPPING"],"prefix":"10.1142","volume":"03","author":[{"given":"XIANG-SUN","family":"ZHANG","sequence":"first","affiliation":[{"name":"Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China"}]},{"given":"YONG","family":"WANG","sequence":"additional","affiliation":[{"name":"Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China"}]},{"given":"ZHONG-WEI","family":"ZHAN","sequence":"additional","affiliation":[{"name":"Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China"}]},{"given":"LING-YUN","family":"WU","sequence":"additional","affiliation":[{"name":"Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China"}]},{"given":"LUONAN","family":"CHEN","sequence":"additional","affiliation":[{"name":"Osaka Sangyo University, Nakagaito 3-1-1, Daito, Osaka 574-8530, Japan"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1089\/106652702760277345"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560040401"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1021\/ma00200a030"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990101)34:1<113::AID-PROT9>3.0.CO;2-J"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10239"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.1998.5.423"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/0893-6080(88)90002-0"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1007\/BF00337288"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1016\/S0305-0548(99)00065-9"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1126\/science.273.5275.666"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1002\/net.3230190602"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1007\/BF00202610"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1016\/0893-6080(95)00033-V"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1023\/A:1016225010659"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560061011"},{"key":"rf19","first-page":"1935","volume":"115","author":"Benjamin P.","journal-title":"J. Che. Phys."},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.1158"},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.92.1.146"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth467"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720005001107","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T17:10:52Z","timestamp":1565197852000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720005001107"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4]]},"references-count":19,"journal-issue":{"issue":"02","published-online":{"date-parts":[[2011,11,21]]},"published-print":{"date-parts":[[2005,4]]}},"alternative-id":["10.1142\/S0219720005001107"],"URL":"https:\/\/doi.org\/10.1142\/s0219720005001107","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,4]]}}}