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First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13\u201355 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.<\/jats:p>","DOI":"10.1016\/s1672-0229(06)60018-1","type":"journal-article","created":{"date-parts":[[2006,4,19]],"date-time":"2006-04-19T17:45:22Z","timestamp":1145468722000},"page":"61-66","source":"Crossref","is-referenced-by-count":0,"title":["A Quasi-Physical Algorithm for the Structure Optimization in an Off-Lattice Protein Model"],"prefix":"10.1093","volume":"4","author":[{"given":"Jing-Fa","family":"Liu","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Huazhong University of Science and Technology , Wuhan, 430074 , China"},{"name":"Department of Mathematics, Hengyang Normal College , Hengyang, 421008 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Qi","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Huazhong University of Science and Technology , Wuhan, 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,4,18]]},"reference":[{"key":"2024051008215821000_bib1","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1021\/bi00327a032","article-title":"Theory for the folding and stability of globular proteins","volume":"24","author":"Dill","year":"1985","journal-title":"Biochemistry"},{"key":"2024051008215821000_bib2","doi-asserted-by":"crossref","first-page":"3986","DOI":"10.1021\/ma00200a030","article-title":"A lattice statistical mechanics model of the conformational and sequence spaces of proteins","volume":"22","author":"Lan","year":"1989","journal-title":"Macromolecules"},{"key":"2024051008215821000_bib3","doi-asserted-by":"crossref","first-page":"3907","DOI":"10.1103\/PhysRevLett.72.3907","article-title":"Proteins with selected sequences fold into unique native conformation","volume":"72","author":"Shakhnovich","year":"1994","journal-title":"Phys. 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