{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T14:28:58Z","timestamp":1777904938743,"version":"3.51.4"},"reference-count":0,"publisher":"SAGE Publications","issue":"2","license":[{"start":{"date-parts":[[2004,7,1]],"date-time":"2004-07-01T00:00:00Z","timestamp":1088640000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["OMICS: A Journal of Integrative Biology"],"published-print":{"date-parts":[[2004,7]]},"abstract":"<jats:p>One of the unsolved paradigms in molecular biology is the protein folding problem. In recent years, with the identification of several diseases as protein folding disorders and with the explosion of genome information and the need for efficient ways to predict protein structure, protein \nfolding became a central issue in molecular sciences research. Using molecular dynamics unfolding simulations of an amyloidogenic protein\u2014transthyretin\u2014as an example, we put forward a series of ideas on how simulations of this type may be used to infer rules and unfolding behavior in \namyloidogenic proteins, and to extrapolate rules for protein folding in different structural classes of proteins. These, in turn, could help in the development of protein structure prediction methods. The need to analyse different proteins and to run multiple simulations creates a huge amount of \ndata which has to be stored, managed, analyzed and shared (database and Grid technology; data mining). Once the data is captured, the next challenge is to find meaningful patterns (associations, correlations, clusters, rules, relationships) among molecular properties, or their relative importance \nat different stages of the folding or unfolding processes. This clearly puts new and interesting challenges to the bioinformatics community.<\/jats:p>","DOI":"10.1089\/1536231041388311","type":"journal-article","created":{"date-parts":[[2004,7,13]],"date-time":"2004-07-13T17:31:46Z","timestamp":1089739906000},"page":"153-166","source":"Crossref","is-referenced-by-count":14,"title":["Protein Folding and Unfolding Simulations: A New Challenge for Data Mining"],"prefix":"10.1177","volume":"8","author":[{"given":"Rui M.M.","family":"Brito","sequence":"first","affiliation":[{"name":"Departamento de Qu\u00edmica, Faculdade de Ci\u00eancias e Tecnologia, and Centro de Neuroci\u00eancias de Coimbra, Universidade de Coimbra, Coimbra, Portugal."}]},{"given":"Werner","family":"Dubitzky","sequence":"additional","affiliation":[]},{"given":"J. Rui","family":"Rodrigues","sequence":"additional","affiliation":[]}],"member":"179","published-online":{"date-parts":[[2004,7]]},"container-title":["OMICS: A Journal of Integrative Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/1536231041388311","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/1536231041388311","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T12:33:21Z","timestamp":1777638801000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.1089\/1536231041388311"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,7]]},"references-count":0,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2004,7]]}},"alternative-id":["10.1089\/1536231041388311"],"URL":"https:\/\/doi.org\/10.1089\/1536231041388311","relation":{},"ISSN":["1536-2310","1557-8100"],"issn-type":[{"value":"1536-2310","type":"print"},{"value":"1557-8100","type":"electronic"}],"subject":[],"published":{"date-parts":[[2004,7]]}}}