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An enhanced fragment library with greater structural diversity is used to expand the search space in the context of fragment-based assembly. To manage the increased complexity of the search space, only a representative subset of the sampled conformations is retained to further guide the search towards the native state. Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols. <\/jats:p>","DOI":"10.1142\/s0219720011005574","type":"journal-article","created":{"date-parts":[[2011,4,26]],"date-time":"2011-04-26T02:07:03Z","timestamp":1303783623000},"page":"383-398","source":"Crossref","is-referenced-by-count":20,"title":["IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH"],"prefix":"10.1142","volume":"09","author":[{"given":"BRIAN","family":"OLSON","sequence":"first","affiliation":[{"name":"Department of Computer Science, George Mason University 4400 University Drive, Fairfax, VA 22030, USA"}]},{"given":"KEVIN","family":"MOLLOY","sequence":"additional","affiliation":[{"name":"Department of Computer Science, George Mason University 4400 University Drive, Fairfax, VA 22030, USA"}]},{"given":"AMARDA","family":"SHEHU","sequence":"additional","affiliation":[{"name":"Department of Computer Science, George Mason University 4400 University Drive, Fairfax, VA 22030, USA"},{"name":"Department of Bioinformatics and Computational Biology, George Mason University 4400 University Drive, Fairfax, VA 22030, USA"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1126\/science.181.4096.223"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1749933"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0197-10"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1038\/438036a"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.37.092707.153558"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1126\/science.1113801"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0607-466"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2003.12.008"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1110\/ps.03154503"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21371"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2007.10.005"},{"key":"rf12","unstructured":"A.\u00a0Shehu, Robotics: Science and Systems V, eds. 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