{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T23:10:06Z","timestamp":1735773006025,"version":"3.32.0"},"reference-count":48,"publisher":"Wiley","issue":"14","license":[{"start":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T00:00:00Z","timestamp":1119571200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Concurrency and Computation"],"published-print":{"date-parts":[[2005,12,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The protein\u2010folding problem is a study of how a protein dynamically folds to its so\u2010called native state\u2014an energetically stable, three\u2010dimensional conformation. Understanding this process is of great practical importance since some devastating diseases such as Alzheimer's and bovine spongiform encephalopathy (Mad Cow) are associated with the misfolding of proteins. We have developed a new computational technique for studying protein folding that is based on probabilistic roadmap methods for motion planning. Our technique yields an approximate map of a protein's potential energy landscape that contains thousands of feasible folding pathways. We have validated our method against known experimental results. Other simulation techniques, such as molecular dynamics or Monte Carlo methods, require many orders of magnitude more time to produce a single, partial trajectory. In this paper we report on our experiences parallelizing our method using STAPL (Standard Template Adaptive Parallel Library) that is being developed in the Parasol Lab at Texas A&amp;M. An efficient parallel version will enable us to study larger proteins with increased accuracy. We demonstrate how STAPL enables portable efficiency across multiple platforms, ranging from small Linux clusters to massively parallel machines such as IBM's BlueGene\/L, without user code modification. Copyright \u00a9 2005 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/cpe.950","type":"journal-article","created":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T20:16:50Z","timestamp":1119644210000},"page":"1643-1656","source":"Crossref","is-referenced-by-count":5,"title":["Parallel protein folding with STAPL"],"prefix":"10.1002","volume":"17","author":[{"given":"Shawna","family":"Thomas","sequence":"first","affiliation":[]},{"given":"Gabriel","family":"Tanase","sequence":"additional","affiliation":[]},{"given":"Lucia K.","family":"Dale","sequence":"additional","affiliation":[]},{"given":"Jose M.","family":"Moreira","sequence":"additional","affiliation":[]},{"given":"Lawrence","family":"Rauchwerger","sequence":"additional","affiliation":[]},{"given":"Nancy M.","family":"Amato","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2005,6,24]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.66.1.549"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.cs.03.060188.000423"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.7.3342"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1089\/10665270252935395"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1089\/10665270360688002"},{"key":"e_1_2_1_7_2","doi-asserted-by":"crossref","unstructured":"SongG ThomasSL DillKA ScholtzJM AmatoNM.A path planning\u2010based study of protein folding with a case study of hairpin formation in protein G and L.Proceedings of the Pacific Symposium of Biocomputing (PSB) 2003;240\u2013251.","DOI":"10.1142\/9789812776303_0023"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1109\/70.508439"},{"key":"e_1_2_1_9_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.8.8.1571"},{"key":"e_1_2_1_10_2","doi-asserted-by":"crossref","unstructured":"AmatoNM DaleLK.Probabilistic roadmap methods are embarrassingly parallel.Proceedings of the IEEE International Conference on Robotics and Automation (ICRA) 1999;688\u2013694.","DOI":"10.1109\/ROBOT.1999.770055"},{"key":"e_1_2_1_11_2","unstructured":"AnP JulaA RusS SaundersS SmithT TanaseG ThomasN AmatoN RauchwergerL.STAPL: An adaptive generic parallel programming library for C++.Proceedings of the 14th International Workshop on Languages and Compilers for Parallel Computing (LCPC) Cumberland Falls KY August2001."},{"key":"e_1_2_1_12_2","doi-asserted-by":"crossref","unstructured":"RauchwergerL ArzuF OuchiK.Standard Templates Adaptive Parallel Library.Proceedings of the 4th International Workshop on Languages Compilers and Run\u2010Time Systems for Scalable Computers (LCR) Pittsburgh PA May1998.","DOI":"10.1007\/3-540-49530-4_32"},{"key":"e_1_2_1_13_2","doi-asserted-by":"crossref","unstructured":"SaundersS RauchwergerL.ARMI: An adaptive platform independent communication library.ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP) San Diego CA June2003.","DOI":"10.1145\/781498.781534"},{"volume-title":"STL Tutorial and Reference Guide","year":"2001","author":"Musser D","key":"e_1_2_1_14_2"},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340210302"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/253694a0"},{"key":"e_1_2_1_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/8.8.769"},{"key":"e_1_2_1_18_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bb.22.060193.002033"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.282.5389.740"},{"volume-title":"Molecular Dynamics Simulation: Elementary Methods","year":"1992","author":"Haile JM","key":"e_1_2_1_20_2"},{"key":"e_1_2_1_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(83)80129-6"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340140310"},{"key":"e_1_2_1_23_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340180405"},{"key":"e_1_2_1_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.91.10.4436"},{"key":"e_1_2_1_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560020508"},{"key":"e_1_2_1_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.20.11305"},{"key":"e_1_2_1_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/35011000"},{"key":"e_1_2_1_28_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.11.5872"},{"key":"e_1_2_1_29_2","doi-asserted-by":"crossref","unstructured":"ApaydinMS BrutlagDL GuestrinC HsuD LatombeJ\u2010C.Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion.Proceedings of the International Conference on Computational Molecular Biology (RECOMB) 2002;12\u201321.","DOI":"10.1145\/565196.565199"},{"key":"e_1_2_1_30_2","doi-asserted-by":"crossref","unstructured":"ApaydinMC SinghAP BrutlagDL LatombeJ\u2010C.Capturing molecular energy landscapes with probabilistic conformational roadmaps.Proceedings of the IEEE International Conference on Robotics and Automation (ICRA) 2001;932\u2013939.","DOI":"10.1109\/ROBOT.2001.932670"},{"key":"e_1_2_1_31_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4615-4022-9"},{"key":"e_1_2_1_32_2","doi-asserted-by":"publisher","DOI":"10.1109\/TC.1983.1676196"},{"key":"e_1_2_1_33_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1007907925007"},{"key":"e_1_2_1_34_2","doi-asserted-by":"publisher","DOI":"10.1007\/3-540-44863-2_6"},{"key":"e_1_2_1_35_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540020311"},{"key":"e_1_2_1_36_2","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.1999.6201"},{"key":"e_1_2_1_37_2","doi-asserted-by":"publisher","DOI":"10.1177\/109434209601000401"},{"key":"e_1_2_1_38_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.10219"},{"key":"e_1_2_1_39_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.290.5498.1903"},{"key":"e_1_2_1_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01160"},{"key":"e_1_2_1_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00997-X"},{"key":"e_1_2_1_42_2","doi-asserted-by":"crossref","unstructured":"Lozano\u2010P\u00e9rezT O'DonnellP.Parallel robot motion planning.Proceedings of the IEEE International Conference on Robotics and Automation (ICRA) 1991;1000\u20131007.","DOI":"10.1109\/ROBOT.1991.131722"},{"key":"e_1_2_1_43_2","doi-asserted-by":"crossref","unstructured":"ChallouDJ GiniM KumarV.Parallel search algorithms for robot motion planning.Proceedings of the IEEE International Conference on Robotics and Automation (ICRA) 1993;46\u201351.","DOI":"10.1109\/ROBOT.1993.292122"},{"key":"e_1_2_1_44_2","doi-asserted-by":"crossref","unstructured":"ChallouD BoleyD GiniM KumarV.A parallel formulation of informed randomized search for robot motion planning problems.Proceedings of the IEEE International Conference on Robotics and Automation (ICRA) 1995;709\u2013714.","DOI":"10.1109\/ROBOT.1995.525367"},{"key":"e_1_2_1_45_2","doi-asserted-by":"publisher","DOI":"10.1177\/027836499101000604"},{"key":"e_1_2_1_46_2","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780199634972.001.0001","volume-title":"Protein Structure Prediction","author":"Sternberg MJ","year":"1996"},{"key":"e_1_2_1_47_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.464068"},{"key":"e_1_2_1_48_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N"},{"key":"e_1_2_1_49_2","unstructured":"BlellochG.NESL: A nested data\u2010parallel language.Technical Report CMU\u2010CS\u201093\u2010129 Carnegie Mellon University April1993."}],"container-title":["Concurrency and Computation: Practice and Experience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fcpe.950","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpe.950","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T22:32:00Z","timestamp":1735770720000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/cpe.950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,6,24]]},"references-count":48,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2005,12,10]]}},"alternative-id":["10.1002\/cpe.950"],"URL":"https:\/\/doi.org\/10.1002\/cpe.950","archive":["Portico"],"relation":{},"ISSN":["1532-0626","1532-0634"],"issn-type":[{"type":"print","value":"1532-0626"},{"type":"electronic","value":"1532-0634"}],"subject":[],"published":{"date-parts":[[2005,6,24]]}}}