{"id":"https://openalex.org/W2036826180","doi":"https://doi.org/10.1186/1751-0473-3-1","title":"Faunus: An object oriented framework for molecular simulation","display_name":"Faunus: An object oriented framework for molecular simulation","publication_year":2008,"publication_date":"2008-02-01","ids":{"openalex":"https://openalex.org/W2036826180","doi":"https://doi.org/10.1186/1751-0473-3-1","mag":"2036826180","pmid":"https://pubmed.ncbi.nlm.nih.gov/18241331"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-3-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-3-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-3-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052083864","display_name":"Mikael Lund","orcid":"https://orcid.org/0000-0001-8178-8175"},"institutions":[{"id":"https://openalex.org/I202391551","display_name":"Czech Academy of Sciences","ror":"https://ror.org/053avzc18","country_code":"CZ","type":"government","lineage":["https://openalex.org/I202391551"]},{"id":"https://openalex.org/I4210145889","display_name":"Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry","ror":"https://ror.org/04nfjn472","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210145889"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Mikael Lund","raw_affiliation_strings":["Institute of Organic Chemistry and Biochemistry, The Academy of Sciences of the Czech Republic, Flemingovo nam,2, CZ-16610 Prague 6, Czech Republic. mlund@mac.com","Institute of Organic Chemistry and Biochemistry, The Academy of Sciences of the Czech Republic, Prague 6, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry, The Academy of Sciences of the Czech Republic, Flemingovo nam,2, CZ-16610 Prague 6, Czech Republic. mlund@mac.com","institution_ids":["https://openalex.org/I4210145889"]},{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry, The Academy of Sciences of the Czech Republic, Prague 6, Czech Republic","institution_ids":["https://openalex.org/I202391551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007907391","display_name":"Martin Trulsson","orcid":"https://orcid.org/0000-0002-5398-9145"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Martin Trulsson","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Lund, P.O.B 124, SE-22100, Lund, Sweden","Department of Theoretical Chemistry University of Lund,Lund,Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Lund, P.O.B 124, SE-22100, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Theoretical Chemistry University of Lund,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5104061358","display_name":"Bj\u00f6rn Persson","orcid":null},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn Persson","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Lund, P.O.B 124, SE-22100, Lund, Sweden","Department of Theoretical Chemistry University of Lund,Lund,Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Lund, P.O.B 124, SE-22100, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Theoretical Chemistry University of Lund,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052083864"],"corresponding_institution_ids":["https://openalex.org/I202391551","https://openalex.org/I4210145889"],"apc_list":null,"apc_paid":null,"fwci":1.6848,"has_fulltext":true,"cited_by_count":160,"citation_normalized_percentile":{"value":0.83160637,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"3","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9187999963760376,"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":0.9187999963760376,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.009999999776482582,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.00989999994635582,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8468061685562134},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7133533954620361},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6750572919845581},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.6019612550735474},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.5125086307525635},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5073382258415222},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4410705864429474},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.43346452713012695},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.4129635691642761},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.40825051069259644},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3441891670227051},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3224928379058838},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19635802507400513}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8468061685562134},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7133533954620361},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6750572919845581},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.6019612550735474},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.5125086307525635},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5073382258415222},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4410705864429474},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.43346452713012695},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4129635691642761},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.40825051069259644},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3441891670227051},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3224928379058838},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19635802507400513},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1751-0473-3-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-3-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:18241331","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18241331","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:doaj.org/article:960edc3a39f241589d81b862eeec32b9","is_oa":false,"landing_page_url":"https://doaj.org/article/960edc3a39f241589d81b862eeec32b9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code for Biology and Medicine, Vol 3, Iss 1, p 1 (2008)","raw_type":"article"},{"id":"pmh:oai:lup.lub.lu.se:cf97eb56-7a06-4555-9335-24f1c395077a","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/1278257","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1751-0473","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2266748","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2266748","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-3-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-3-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320307844","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2036826180.pdf","grobid_xml":"https://content.openalex.org/works/W2036826180.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1972197313","https://openalex.org/W1981021420","https://openalex.org/W1981413816","https://openalex.org/W1988888548","https://openalex.org/W1995436342","https://openalex.org/W2001067678","https://openalex.org/W2011435358","https://openalex.org/W2018058849","https://openalex.org/W2029667189","https://openalex.org/W2035720425","https://openalex.org/W2047576169","https://openalex.org/W2056760934","https://openalex.org/W2094007707","https://openalex.org/W2095159785","https://openalex.org/W2104301310","https://openalex.org/W2118980032","https://openalex.org/W2507772696","https://openalex.org/W2913602891","https://openalex.org/W2987803397"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2329643025","https://openalex.org/W3131163342","https://openalex.org/W2166271660","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2002770077","https://openalex.org/W2361728394","https://openalex.org/W2352631095","https://openalex.org/W2408577762"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,58,92],"present":[2],"a":[3,54,82,112],"C++":[4,84,104],"class":[5],"library":[6],"for":[7,75,115],"Monte":[8],"Carlo":[9],"simulation":[10],"of":[11,42,121],"molecular":[12,76,117],"systems,":[13],"including":[14],"proteins":[15],"in":[16,81,131],"solution.":[17],"The":[18,33],"design":[19,64],"is":[20,79],"generic":[21,116],"and":[22,105],"highly":[23],"modular,":[24],"enabling":[25],"multiple":[26],"developers":[27],"to":[28,51,68,98,137],"easily":[29],"implement":[30],"additional":[31],"features.":[32],"statistical":[34],"mechanical":[35],"methods":[36],"are":[37,49],"documented":[38],"by":[39],"extensive":[40],"use":[41],"code":[43,122],"comments":[44,126],"that":[45,86,132],"-":[46,48],"subsequently":[47],"collected":[50],"automatically":[52],"build":[53],"web-based":[55],"manual.":[56],"RESULTS:":[57],"show":[59],"how":[60],"an":[61,70],"object":[62],"oriented":[63],"can":[65,87],"be":[66,138],"used":[67],"create":[69],"intuitively":[71],"appealing":[72],"coding":[73,101],"framework":[74],"simulation.":[77],"This":[78],"exemplified":[80],"minimalistic":[83],"program":[85],"calculate":[88],"protein":[89],"protonation":[90],"states.":[91],"further":[93],"discuss":[94],"performance":[95],"issues":[96],"related":[97],"high":[99],"level":[100],"abstraction.":[102],"CONCLUSION:":[103],"the":[106],"Standard":[107],"Template":[108],"Library":[109],"(STL)":[110],"provide":[111],"high-performance":[113],"platform":[114],"modeling.":[118],"Automatic":[119],"generation":[120],"documentation":[123],"from":[124],"inline":[125],"has":[127],"proven":[128],"particularly":[129],"useful":[130],"no":[133],"separate":[134],"manual":[135],"needs":[136],"maintained.":[139]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":32},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
