{"id":"https://openalex.org/W2062037031","doi":"https://doi.org/10.1155/2012/674832","title":"Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules","display_name":"Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules","publication_year":2012,"publication_date":"2012-12-04","ids":{"openalex":"https://openalex.org/W2062037031","doi":"https://doi.org/10.1155/2012/674832","mag":"2062037031"},"language":"en","primary_location":{"id":"doi:10.1155/2012/674832","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/674832","pdf_url":"https://downloads.hindawi.com/archive/2012/674832.pdf","source":{"id":"https://openalex.org/S2788495","display_name":"Advances in Artificial Intelligence","issn_l":"1687-7470","issn":["1687-7470","1687-7489"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/archive/2012/674832.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059509977","display_name":"Brian Olson","orcid":"https://orcid.org/0000-0001-6381-9281"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Olson","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062343708","display_name":"Irina Hashmi","orcid":null},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Irina Hashmi","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103139709","display_name":"Kevin Molloy","orcid":"https://orcid.org/0000-0002-9859-7604"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Molloy","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044722808","display_name":"Amarda Shehu","orcid":"https://orcid.org/0000-0001-5230-4610"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amarda Shehu","raw_affiliation_strings":["Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA","Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044722808"],"corresponding_institution_ids":["https://openalex.org/I162714631"],"apc_list":null,"apc_paid":null,"fwci":1.3407,"has_fulltext":true,"cited_by_count":92,"citation_normalized_percentile":{"value":0.79643335,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"2012","issue":null,"first_page":"1","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9901000261306763,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.8601858615875244},{"id":"https://openalex.org/keywords/packing-problems","display_name":"Packing problems","score":0.627985954284668},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6086024641990662},{"id":"https://openalex.org/keywords/characterization","display_name":"Characterization (materials science)","score":0.5318301320075989},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5122200846672058},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4805472493171692},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.43673068284988403},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.42819300293922424},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.4231576919555664},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.39216405153274536},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3349594473838806},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3144373297691345},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2472676932811737},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21337813138961792},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19085991382598877},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.16843417286872864},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16190829873085022},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.12756618857383728},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.08594772219657898}],"concepts":[{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.8601858615875244},{"id":"https://openalex.org/C130253271","wikidata":"https://www.wikidata.org/wiki/Q3851477","display_name":"Packing problems","level":2,"score":0.627985954284668},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6086024641990662},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.5318301320075989},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5122200846672058},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4805472493171692},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.43673068284988403},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.42819300293922424},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.4231576919555664},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.39216405153274536},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3349594473838806},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3144373297691345},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2472676932811737},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21337813138961792},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19085991382598877},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.16843417286872864},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16190829873085022},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.12756618857383728},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08594772219657898},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1155/2012/674832","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/674832","pdf_url":"https://downloads.hindawi.com/archive/2012/674832.pdf","source":{"id":"https://openalex.org/S2788495","display_name":"Advances in Artificial Intelligence","issn_l":"1687-7470","issn":["1687-7470","1687-7489"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1155/2012/674832","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/674832","pdf_url":"https://downloads.hindawi.com/archive/2012/674832.pdf","source":{"id":"https://openalex.org/S2788495","display_name":"Advances in Artificial Intelligence","issn_l":"1687-7470","issn":["1687-7470","1687-7489"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G2230820996","display_name":null,"funder_award_id":"1144106","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G575763840","display_name":null,"funder_award_id":"1016995","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2062037031.pdf","grobid_xml":"https://content.openalex.org/works/W2062037031.grobid-xml"},"referenced_works_count":102,"referenced_works":["https://openalex.org/W48766992","https://openalex.org/W75245544","https://openalex.org/W1482298744","https://openalex.org/W1490138956","https://openalex.org/W1521785144","https://openalex.org/W1528066505","https://openalex.org/W1535028232","https://openalex.org/W1535422202","https://openalex.org/W1583958742","https://openalex.org/W1606954097","https://openalex.org/W1965660671","https://openalex.org/W1966388861","https://openalex.org/W1967607711","https://openalex.org/W1968901680","https://openalex.org/W1971725855","https://openalex.org/W1979591743","https://openalex.org/W1980571928","https://openalex.org/W1981581073","https://openalex.org/W1982609064","https://openalex.org/W1983036219","https://openalex.org/W1983102499","https://openalex.org/W1985006546","https://openalex.org/W1986602910","https://openalex.org/W1987104859","https://openalex.org/W1989161865","https://openalex.org/W1991934839","https://openalex.org/W1993018469","https://openalex.org/W1995808589","https://openalex.org/W1998367993","https://openalex.org/W2004461664","https://openalex.org/W2005303043","https://openalex.org/W2008067788","https://openalex.org/W2011220582","https://openalex.org/W2012364120","https://openalex.org/W2013785414","https://openalex.org/W2014095962","https://openalex.org/W2014948872","https://openalex.org/W2015403140","https://openalex.org/W2016423785","https://openalex.org/W2017509211","https://openalex.org/W2021478732","https://openalex.org/W2024060531","https://openalex.org/W2027638447","https://openalex.org/W2028344520","https://openalex.org/W2030148200","https://openalex.org/W2039366512","https://openalex.org/W2042083778","https://openalex.org/W2042730255","https://openalex.org/W2046002103","https://openalex.org/W2047602629","https://openalex.org/W2049269366","https://openalex.org/W2053599146","https://openalex.org/W2054549458","https://openalex.org/W2056760934","https://openalex.org/W2057350662","https://openalex.org/W2061095840","https://openalex.org/W2062166748","https://openalex.org/W2063831812","https://openalex.org/W2065247480","https://openalex.org/W2065656981","https://openalex.org/W2066283432","https://openalex.org/W2076600143","https://openalex.org/W2077412035","https://openalex.org/W2077743314","https://openalex.org/W2079871896","https://openalex.org/W2085549906","https://openalex.org/W2093984919","https://openalex.org/W2096506888","https://openalex.org/W2102713507","https://openalex.org/W2104940206","https://openalex.org/W2110483430","https://openalex.org/W2112615307","https://openalex.org/W2112959255","https://openalex.org/W2115540209","https://openalex.org/W2115617797","https://openalex.org/W2115889893","https://openalex.org/W2118180037","https://openalex.org/W2119394534","https://openalex.org/W2124106603","https://openalex.org/W2125213515","https://openalex.org/W2126551164","https://openalex.org/W2128736063","https://openalex.org/W2133312040","https://openalex.org/W2139183106","https://openalex.org/W2139257751","https://openalex.org/W2141233921","https://openalex.org/W2144288821","https://openalex.org/W2144689095","https://openalex.org/W2150192011","https://openalex.org/W2151269585","https://openalex.org/W2151460035","https://openalex.org/W2152537652","https://openalex.org/W2160721947","https://openalex.org/W2161151688","https://openalex.org/W2162166182","https://openalex.org/W2169267213","https://openalex.org/W2295145325","https://openalex.org/W2952971819","https://openalex.org/W3105405267","https://openalex.org/W3105621768","https://openalex.org/W3199104097","https://openalex.org/W3204855000"],"related_works":["https://openalex.org/W2091418430","https://openalex.org/W2153731865","https://openalex.org/W2471196694","https://openalex.org/W2127982566","https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2158562723","https://openalex.org/W2058542300"],"abstract_inverted_index":{"Since":[0],"its":[1,50,96],"introduction,":[2],"the":[3,58,73,86,113,126,167],"basin":[4],"hopping":[5],"(BH)":[6],"framework":[7,75],"has":[8],"proven":[9],"useful":[10],"for":[11],"hard":[12],"nonlinear":[13],"optimization":[14],"problems":[15,28,83],"with":[16,148],"multiple":[17],"variables":[18],"and":[19,78,92,134],"modalities.":[20],"Applications":[21],"span":[22],"a":[23,42,54,103,157,163],"wide":[24],"range,":[25],"from":[26],"packing":[27],"in":[29,36,44,62,102,116,125,156],"geometry":[30],"to":[31,49,52,81,85,95,99],"characterization":[32,87,168],"of":[33,57,64,88,112,128,169],"molecular":[34],"states":[35,155],"statistical":[37],"physics.":[38],"BH":[39,74,117,142],"is":[40,76],"seeing":[41],"reemergence":[43],"computational":[45],"structural":[46],"biology":[47],"due":[48,94],"ability":[51,98],"obtain":[53],"coarse-grained":[55],"representation":[56],"protein":[59,89,131,158],"energy":[60],"surface":[61],"terms":[63],"local":[65],"minima.":[66],"In":[67],"this":[68],"paper,":[69],"we":[70],"show":[71,108,140],"that":[72,121,141],"general":[77],"versatile,":[79],"allowing":[80],"address":[82],"related":[84,147],"structure,":[90],"assembly,":[91],"motion":[93],"fundamental":[97],"sample":[100],"minima":[101,146],"high-dimensional":[104],"variable":[105],"space.":[106],"We":[107,138],"how":[109],"specific":[110],"implementations":[111],"main":[114],"components":[115],"yield":[118],"algorithmic":[119],"realizations":[120],"attain":[122],"state-of-the-art":[123],"results":[124],"context":[127],"ab":[129],"initio":[130],"structure":[132],"prediction":[133],"rigid":[135],"protein-protein":[136],"docking.":[137],"also":[139],"can":[143],"map":[144],"intermediate":[145],"motions":[149],"connecting":[150,172],"diverse":[151],"stable":[152],"functionally":[153],"relevant":[154],"molecule,":[159],"thus":[160],"serving":[161],"as":[162],"first":[164],"step":[165],"towards":[166],"transition":[170],"trajectories":[171],"these":[173],"states.":[174]},"counts_by_year":[{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":6}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
