{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T03:48:19Z","timestamp":1774842499231,"version":"3.50.1"},"reference-count":159,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2012,2,13]],"date-time":"2012-02-13T00:00:00Z","timestamp":1329091200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>Unlike the secondary structure elements that connect in protein structures, loop fragments in protein chains are often highly mobile even in generally stable proteins. The structural variability of loops is often at the center of a protein\u2019s stability, folding, and even biological function. Loops are found to mediate important biological processes, such as signaling, protein-ligand binding, and protein-protein interactions. Modeling conformations of a loop under physiological conditions remains an open problem in computational biology. This article reviews computational research in loop modeling, highlighting progress and challenges. Important insight is obtained on potential directions for future research.<\/jats:p>","DOI":"10.3390\/e14020252","type":"journal-article","created":{"date-parts":[[2012,2,13]],"date-time":"2012-02-13T11:17:45Z","timestamp":1329131865000},"page":"252-290","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Modeling Structures and Motions of Loops in Protein Molecules"],"prefix":"10.3390","volume":"14","author":[{"given":"Amarda","family":"Shehu","sequence":"first","affiliation":[{"name":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"},{"name":"Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lydia E.","family":"Kavraki","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Rice University, Houston, TX 77005, USA"},{"name":"Department of Bioengineering, Rice University, Houston, TX 77005, USA"},{"name":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2012,2,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"Anfinsen","year":"1973","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6679","DOI":"10.1073\/pnas.0408930102","article-title":"Molecular Dynamics and protein function","volume":"102","author":"Karplus","year":"2005","journal-title":"Proc. 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