{"id":"https://openalex.org/W2140796042","doi":"https://doi.org/10.1093/bioinformatics/btt051","title":"MSMExplorer: visualizing Markov state models for biomolecule folding simulations","display_name":"MSMExplorer: visualizing Markov state models for biomolecule folding simulations","publication_year":2013,"publication_date":"2013-01-30","ids":{"openalex":"https://openalex.org/W2140796042","doi":"https://doi.org/10.1093/bioinformatics/btt051","mag":"2140796042","pmid":"https://pubmed.ncbi.nlm.nih.gov/23365411"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/7/950/701833/btt051.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/7/950/701833/btt051.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073502088","display_name":"Bryce Cronkite-Ratcliff","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bryce Cronkite-Ratcliff","raw_affiliation_strings":["1 Department of Computer Science, 2Department of Chemistry and 3Department of Structural Biology, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, 2Department of Chemistry and 3Department of Structural Biology, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032418986","display_name":"Vijay S. Pande","orcid":"https://orcid.org/0000-0003-2774-1178"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijay Pande","raw_affiliation_strings":["1 Department of Computer Science, 2Department of Chemistry and 3Department of Structural Biology, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, 2Department of Chemistry and 3Department of Structural Biology, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073502088"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.7215,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.9187989,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"29","issue":"7","first_page":"950","last_page":"952"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.98089998960495,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.6588394641876221},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6254705190658569},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6140419244766235},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.5201364159584045},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.5164589881896973},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.4333471953868866},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3967452049255371},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.355781227350235},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35237109661102295},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.29021981358528137},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.1911706030368805},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.18425294756889343},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1540621519088745},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13241755962371826},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12458038330078125},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.06258174777030945}],"concepts":[{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.6588394641876221},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6254705190658569},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6140419244766235},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.5201364159584045},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.5164589881896973},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.4333471953868866},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3967452049255371},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.355781227350235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35237109661102295},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29021981358528137},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.1911706030368805},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18425294756889343},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1540621519088745},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13241755962371826},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12458038330078125},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.06258174777030945},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/7/950/701833/btt051.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23365411","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23365411","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/7/950/701833/btt051.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140796042.pdf","grobid_xml":"https://content.openalex.org/works/W2140796042.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1967722756","https://openalex.org/W1969903391","https://openalex.org/W2066795144","https://openalex.org/W2080076400","https://openalex.org/W2125910575","https://openalex.org/W2155142785","https://openalex.org/W2158323088","https://openalex.org/W2165741325","https://openalex.org/W2167482691","https://openalex.org/W2169528473","https://openalex.org/W2184417913","https://openalex.org/W3022981850","https://openalex.org/W6777060225"],"related_works":["https://openalex.org/W2084326697","https://openalex.org/W2027903142","https://openalex.org/W2354322608","https://openalex.org/W2804608325","https://openalex.org/W2077211377","https://openalex.org/W2186675474","https://openalex.org/W2387462590","https://openalex.org/W2056274461","https://openalex.org/W2368739446","https://openalex.org/W2010321967"],"abstract_inverted_index":{"MSMExplorer":[0],"is":[1,10],"available":[2,12],"for":[3],"download":[4],"from":[5],"https://simtk.org/home/msmexplorer.":[6],"The":[7],"source":[8],"code":[9],"made":[11],"under":[13],"the":[14],"GNU":[15],"Lesser":[16],"General":[17],"Public":[18],"License":[19],"at":[20],"https://github.com/SimTk/msmexplorer.":[21]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}