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We have developed an algorithm for generating the conformations of candidate loops that fit in a gap of given length in a protein structure framework. Our method proceeds by concatenating small fragments of protein chosen from small libraries of representative fragments. Our approach has the advantages of ab initio methods since we are able to enumerate all candidate loops in the discrete approximation of the conformational space accessible to the loop, as well as the advantages of database search approach since the use of fragments of known protein structures guarantees that the backbone conformations are physically reasonable. We test our approach on a set of 427 loops, varying in length from four residues to 14 residues. The quality of the candidate loops is evaluated in terms of global coordinate root mean square (cRMS). The top predictions vary between 0.3 and 4.2 \u00c5 for four-residue loops and between 1.5 and 3.1 \u00c5 for 14-residue loops, respectively.<\/jats:p>","DOI":"10.1177\/0278364905050352","type":"journal-article","created":{"date-parts":[[2005,1,26]],"date-time":"2005-01-26T07:27:56Z","timestamp":1106724476000},"page":"151-163","source":"Crossref","is-referenced-by-count":58,"title":["Inverse Kinematics in Biology: The Protein Loop Closure Problem"],"prefix":"10.1177","volume":"24","author":[{"given":"Rachel","family":"Kolodny","sequence":"first","affiliation":[{"name":"Department of Structural Biology and Computer Science Department,                         Stanford University, Stanford, CA 94305, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leonidas","family":"Guibas","sequence":"additional","affiliation":[{"name":"Computer Science Department, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Levitt","sequence":"additional","affiliation":[{"name":"Department of Structural Biology, Stanford University, Stanford, CA                         94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrice","family":"Koehl","sequence":"additional","affiliation":[{"name":"Department of Structural Biology, Stanford University, Stanford, CA                         94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2005,2,1]]},"reference":[{"key":"atypb1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"atypb2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"atypb3","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(77)80200-3"},{"key":"atypb4","doi-asserted-by":"crossref","unstructured":"Bonneau, R., and Baker, D. 2001. 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