{"id":"https://openalex.org/W4362691831","doi":"https://doi.org/10.1021/acs.jcim.2c01296","title":"BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations","display_name":"BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations","publication_year":2023,"publication_date":"2023-04-07","ids":{"openalex":"https://openalex.org/W4362691831","doi":"https://doi.org/10.1021/acs.jcim.2c01296","pmid":"https://pubmed.ncbi.nlm.nih.gov/37027181"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01296","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01296","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10278562/pdf/nihms-1901154.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028185893","display_name":"Robert M. Raddi","orcid":"https://orcid.org/0000-0001-7139-5028"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert M. Raddi","raw_affiliation_strings":["Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States"],"raw_orcid":"https://orcid.org/0000-0001-7139-5028","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088783242","display_name":"Ge Yunhui","orcid":"https://orcid.org/0000-0002-3946-1440"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunhui Ge","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-3946-1440","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074806960","display_name":"Vincent A. Voelz","orcid":"https://orcid.org/0000-0002-1054-2124"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vincent A. Voelz","raw_affiliation_strings":["Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States"],"raw_orcid":"https://orcid.org/0000-0002-1054-2124","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074806960"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":null,"apc_paid":null,"fwci":1.3498,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.80330998,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"63","issue":"8","first_page":"2370","last_page":"2381"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9993000030517578,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.996399998664856,"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/computer-science","display_name":"Computer science","score":0.6844916343688965},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6378896832466125},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5387289524078369},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4885340929031372},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.4752005338668823},{"id":"https://openalex.org/keywords/gibbs-sampling","display_name":"Gibbs sampling","score":0.4623291492462158},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.428314208984375},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38873881101608276},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14715197682380676}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6844916343688965},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6378896832466125},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5387289524078369},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4885340929031372},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4752005338668823},{"id":"https://openalex.org/C158424031","wikidata":"https://www.wikidata.org/wiki/Q1191905","display_name":"Gibbs sampling","level":3,"score":0.4623291492462158},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.428314208984375},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38873881101608276},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14715197682380676}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.2c01296","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01296","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37027181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37027181","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10278562","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10278562","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10278562/pdf/nihms-1901154.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10278562","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10278562","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10278562/pdf/nihms-1901154.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2707551821","display_name":null,"funder_award_id":"S10 OD020095","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3260570889","display_name":null,"funder_award_id":"1S10OD020095","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3549313427","display_name":null,"funder_award_id":"R01GM123296","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4412420759","display_name":"MRI: Acquisition of a Flexible High-Performance Computing System for Data and Compute Driven Scientific Discovery","funder_award_id":"1625061","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5259331294","display_name":null,"funder_award_id":"W911NF","funder_id":"https://openalex.org/F4320338295","funder_display_name":"Army Research Laboratory"},{"id":"https://openalex.org/G7589035627","display_name":null,"funder_award_id":"R01 GM123296","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338295","display_name":"Army Research Laboratory","ror":"https://ror.org/011hc8f90"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4362691831.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1894633155","https://openalex.org/W1967025687","https://openalex.org/W1985546344","https://openalex.org/W1986396635","https://openalex.org/W1993555435","https://openalex.org/W2011510351","https://openalex.org/W2015078526","https://openalex.org/W2015367561","https://openalex.org/W2023511762","https://openalex.org/W2024762727","https://openalex.org/W2029120587","https://openalex.org/W2034016778","https://openalex.org/W2042318795","https://openalex.org/W2043970624","https://openalex.org/W2051091550","https://openalex.org/W2052439778","https://openalex.org/W2061144516","https://openalex.org/W2061827156","https://openalex.org/W2067733087","https://openalex.org/W2078162783","https://openalex.org/W2093030571","https://openalex.org/W2100094261","https://openalex.org/W2129762799","https://openalex.org/W2136849653","https://openalex.org/W2147988069","https://openalex.org/W2156313302","https://openalex.org/W2160284256","https://openalex.org/W2180738695","https://openalex.org/W2241089358","https://openalex.org/W2265101181","https://openalex.org/W2512849379","https://openalex.org/W2560026367","https://openalex.org/W2565914957","https://openalex.org/W2566072464","https://openalex.org/W2570104014","https://openalex.org/W2736124076","https://openalex.org/W2790940744","https://openalex.org/W2803396657","https://openalex.org/W2805679697","https://openalex.org/W2889864290","https://openalex.org/W2900977207","https://openalex.org/W2904163250","https://openalex.org/W2906718052","https://openalex.org/W2925663094","https://openalex.org/W2964917500","https://openalex.org/W2973748343","https://openalex.org/W2998739142","https://openalex.org/W3013283700","https://openalex.org/W3102679581","https://openalex.org/W3103293462","https://openalex.org/W3105466755","https://openalex.org/W3105581675","https://openalex.org/W3163051848","https://openalex.org/W3169673449","https://openalex.org/W3171261065"],"related_works":["https://openalex.org/W840335986","https://openalex.org/W2372267530","https://openalex.org/W2146501959","https://openalex.org/W1517763961","https://openalex.org/W1501929113","https://openalex.org/W4303857162","https://openalex.org/W1919985504","https://openalex.org/W3122927555","https://openalex.org/W2965643117","https://openalex.org/W27102384"],"abstract_inverted_index":{"Bayesian":[0],"Inference":[1],"of":[2,19,38,42,92,100],"Conformational":[3],"Populations":[4],"(BICePs)":[5],"version":[6,41],"2.0":[7],"(v2.0)":[8],"is":[9],"a":[10,45,116,127],"free,":[11],"open-source":[12],"Python":[13],"package":[14,50],"that":[15],"reweights":[16],"theoretical":[17,128],"predictions":[18],"conformational":[20],"state":[21],"populations":[22],"using":[23,130],"sparse":[24],"and/or":[25],"noisy":[26],"experimental":[27,64,131],"measurements.":[28,132],"In":[29],"this":[30],"article,":[31],"we":[32],"describe":[33],"the":[34,39,56,93],"implementation":[35],"and":[36,48,74,79,84,98,103,114],"usage":[37],"latest":[40],"BICePs":[43,86,123],"(v2.0),":[44],"powerful,":[46],"user-friendly":[47],"extensible":[49],"which":[51],"makes":[52],"several":[53],"improvements":[54],"upon":[55],"previous":[57],"version.":[58],"The":[59],"algorithm":[60],"now":[61],"supports":[62],"many":[63],"NMR":[65],"observables":[66],"(NOE":[67],"distances,":[68],"chemical":[69],"shifts,":[70],"J":[71],"-coupling":[72],"constants,":[73],"hydrogen\u2013deuterium":[75],"exchange":[76],"protection":[77],"factors),":[78],"enables":[80],"convenient":[81],"data":[82],"preparation":[83],"processing.":[85],"v2.0":[87,124],"can":[88],"perform":[89],"automatic":[90],"analysis":[91],"sampled":[94],"posterior,":[95],"including":[96],"visualization,":[97],"evaluation":[99],"statistical":[101],"significance":[102],"sampling":[104],"convergence.":[105],"We":[106],"provide":[107],"specific":[108],"coding":[109],"examples":[110],"for":[111],"these":[112],"topics,":[113],"present":[115],"detailed":[117],"example":[118],"illustrating":[119],"how":[120],"to":[121,125],"use":[122],"reweight":[126],"ensemble":[129]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-09T07:52:08.696243","created_date":"2025-10-10T00:00:00"}
