{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T00:04:16Z","timestamp":1717891456007},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Loops in proteins are often involved in biochemical functions. Their irregularity and flexibility make experimental structure determination and computational modeling challenging. Most current loop modeling methods focus on modeling single loops. In protein structure prediction, multiple loops often need to be modeled simultaneously. As interactions among loops in spatial proximity can be rather complex, sampling the conformations of multiple interacting loops is a challenging task.<\/jats:p><jats:p>Results: In this study, we report a new method called multi-loop Distance-guided Sequential chain-Growth Monte Carlo (M-DiSGro) for prediction of the conformations of multiple interacting loops in proteins. Our method achieves an average RMSD of 1.93\u2009\u00c5 for lowest energy conformations of 36 pairs of interacting protein loops with the total length ranging from 12 to 24 residues. We further constructed a data set containing proteins with 2, 3 and 4 interacting loops. For the most challenging target proteins with four loops, the average RMSD of the lowest energy conformations is 2.35\u2009\u00c5. Our method is also tested for predicting multiple loops in \u03b2-barrel membrane proteins. For outer-membrane protein G, the lowest energy conformation has a RMSD of 2.62\u2009\u00c5 for the three extracellular interacting loops with a total length of 34 residues (12, 12 and 10 residues in each loop).<\/jats:p><jats:p>Availability and implementation: The software is freely available at: tanto.bioe.uic.edu\/m-DiSGro.<\/jats:p><jats:p>Contact: \u00a0jinfeng@stat.fsu.edu or jliang@uic.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv198","type":"journal-article","created":{"date-parts":[[2015,4,11]],"date-time":"2015-04-11T03:32:53Z","timestamp":1428723173000},"page":"2646-2652","source":"Crossref","is-referenced-by-count":13,"title":["Conformational sampling and structure prediction of multiple interacting loops in soluble and<i>\u03b2<\/i>-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method"],"prefix":"10.1093","volume":"31","author":[{"given":"Ke","family":"Tang","sequence":"first","affiliation":[{"name":"1 Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel W.K.","family":"Wong","sequence":"additional","affiliation":[{"name":"2 Department of Statistics, University of Florida, Gainesville, FL,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"3 Department of Statistics, Harvard University, Science Center, Cambridge, MA and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinfeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"4 Department of Statistics, Florida State University, Tallahassee, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Liang","sequence":"additional","affiliation":[{"name":"1 Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,4,9]]},"reference":[{"key":"2023020202201333400_btv198-B1","article-title":"Archdb 2014: structural classification of loops in proteins","author":"Bonet","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020202201333400_btv198-B2","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1110\/ps.0242703","article-title":"Cyclic coordinate descent: a robotics algorithm for protein loop closure","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci."},{"key":"2023020202201333400_btv198-B3","doi-asserted-by":"crossref","first-page":"025101","DOI":"10.1063\/1.4811286","article-title":"Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method","volume":"139","author":"Cao","year":"2013","journal-title":"J. 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