{"id":"https://openalex.org/W3032569777","doi":"https://doi.org/10.1186/s13321-020-00432-9","title":"MFsim\u2014an open Java all-in-one rich-client simulation environment for mesoscopic simulation","display_name":"MFsim\u2014an open Java all-in-one rich-client simulation environment for mesoscopic simulation","publication_year":2020,"publication_date":"2020-05-01","ids":{"openalex":"https://openalex.org/W3032569777","doi":"https://doi.org/10.1186/s13321-020-00432-9","mag":"3032569777","pmid":"https://pubmed.ncbi.nlm.nih.gov/33430951"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-020-00432-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00432-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00432-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00432-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041754260","display_name":"Karina van den Broek","orcid":"https://orcid.org/0000-0002-9639-7975"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karina van den Broek","raw_affiliation_strings":["Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany","Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0722-4229","affiliations":[{"raw_affiliation_string":"Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany","institution_ids":["https://openalex.org/I62318514"]},{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048630096","display_name":"Mirco Daniel","orcid":"https://orcid.org/0000-0002-8516-8974"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mirco Daniel","raw_affiliation_strings":["Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081925401","display_name":"Matthias Epple","orcid":"https://orcid.org/0000-0002-1641-7068"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Epple","raw_affiliation_strings":["Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047368663","display_name":"Jan-Mathis Hein","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jan-Mathis Hein","raw_affiliation_strings":["Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033169519","display_name":"Hubert Kuhn","orcid":"https://orcid.org/0000-0001-5122-2189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hubert Kuhn","raw_affiliation_strings":["CAM-D Technologies GmbH, Solingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAM-D Technologies GmbH, Solingen, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008120721","display_name":"Stefan Neumann","orcid":"https://orcid.org/0000-0002-3981-1500"},"institutions":[{"id":"https://openalex.org/I4210128066","display_name":"Medizinisch Wissenschaftliche Verlagsgesellschaft (Germany)","ror":"https://ror.org/034tp1f71","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210128066"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Neumann","raw_affiliation_strings":["GNWI - Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany","GNWI \u2013 Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GNWI - Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany","institution_ids":["https://openalex.org/I4210128066"]},{"raw_affiliation_string":"GNWI \u2013 Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090863551","display_name":"Andreas Truszkowski","orcid":null},"institutions":[{"id":"https://openalex.org/I4210144380","display_name":"Yara (Germany)","ror":"https://ror.org/039hegs97","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210144380","https://openalex.org/I67171562"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Truszkowski","raw_affiliation_strings":["Yara Deutschland, D\u00fclmen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yara Deutschland, D\u00fclmen, Germany","institution_ids":["https://openalex.org/I4210144380"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089744377","display_name":"Achim Zielesny","orcid":"https://orcid.org/0000-0003-0722-4229"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Achim Zielesny","raw_affiliation_strings":["Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de","Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5089744377"],"corresponding_institution_ids":["https://openalex.org/I4210148697"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.0597,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73835458,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"29","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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/T10405","display_name":"Advanced Polymer Synthesis and Characterization","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"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/dissipative-particle-dynamics","display_name":"Dissipative particle dynamics","score":0.8957169651985168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.814372181892395},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7322961688041687},{"id":"https://openalex.org/keywords/mesoscopic-physics","display_name":"Mesoscopic physics","score":0.70878005027771},{"id":"https://openalex.org/keywords/testbed","display_name":"Testbed","score":0.5887237787246704},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.44593101739883423},{"id":"https://openalex.org/keywords/modeling-and-simulation","display_name":"Modeling and simulation","score":0.4187874495983124},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.41344916820526123},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.23129749298095703},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2121238112449646},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.14366689324378967},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11285987496376038},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09434923529624939}],"concepts":[{"id":"https://openalex.org/C45594756","wikidata":"https://www.wikidata.org/wiki/Q5282784","display_name":"Dissipative particle dynamics","level":3,"score":0.8957169651985168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.814372181892395},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7322961688041687},{"id":"https://openalex.org/C177731217","wikidata":"https://www.wikidata.org/wiki/Q2622244","display_name":"Mesoscopic physics","level":2,"score":0.70878005027771},{"id":"https://openalex.org/C31395832","wikidata":"https://www.wikidata.org/wiki/Q1318674","display_name":"Testbed","level":2,"score":0.5887237787246704},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.44593101739883423},{"id":"https://openalex.org/C167343916","wikidata":"https://www.wikidata.org/wiki/Q6888384","display_name":"Modeling and simulation","level":2,"score":0.4187874495983124},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.41344916820526123},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.23129749298095703},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2121238112449646},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.14366689324378967},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11285987496376038},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09434923529624939},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-020-00432-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00432-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00432-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:33430951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33430951","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:db4575260b6544c58c614c730b1aab32","is_oa":true,"landing_page_url":"https://doaj.org/article/db4575260b6544c58c614c730b1aab32","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-15 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7195747","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7195747","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-020-00432-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00432-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00432-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.46000000834465027}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3032569777.pdf","grobid_xml":"https://content.openalex.org/works/W3032569777.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1970585263","https://openalex.org/W1971232585","https://openalex.org/W1982220212","https://openalex.org/W1988313573","https://openalex.org/W2004812508","https://openalex.org/W2007040080","https://openalex.org/W2030483511","https://openalex.org/W2030891958","https://openalex.org/W2032655419","https://openalex.org/W2038977497","https://openalex.org/W2093310284","https://openalex.org/W2100827887","https://openalex.org/W2105803236","https://openalex.org/W2110447282","https://openalex.org/W2121452469","https://openalex.org/W2806830112","https://openalex.org/W2885282017"],"related_works":["https://openalex.org/W5012203","https://openalex.org/W2790535609","https://openalex.org/W1995574656","https://openalex.org/W97316223","https://openalex.org/W4240653033","https://openalex.org/W2105095141","https://openalex.org/W2004303496","https://openalex.org/W2187513553","https://openalex.org/W2099138160","https://openalex.org/W1979018979"],"abstract_inverted_index":{"MFsim":[0,95],"is":[1],"an":[2,92],"open":[3,93],"Java":[4],"all-in-one":[5],"rich-client":[6],"computing":[7],"environment":[8,27],"for":[9,19,59,71,97,100],"mesoscopic":[10,35],"simulation":[11,17,36,42,73,80,85],"with":[12,44],"Jdpd":[13],"as":[14],"its":[15],"default":[16],"kernel":[18],"Molecular":[20],"Fragment":[21],"(Dissipative":[22],"Particle)":[23],"Dynamics.":[24],"The":[25],"new":[26],"comprises":[28],"the":[29],"complete":[30],"preparation-simulation-evaluation":[31],"triad":[32],"of":[33,65,103],"a":[34,51,56,63,68],"task":[37],"and":[38,46,78],"especially":[39],"enables":[40],"biomolecular":[41],"tasks":[43],"peptides":[45],"proteins.":[47],"Productive":[48],"highlights":[49],"are":[50],"SPICES":[52],"molecular":[53],"structure":[54],"editor,":[55],"PDB-to-SPICES":[57],"parser":[58],"particle-based":[60],"peptide/protein":[61],"representations,":[62],"support":[64],"polymer":[66],"definitions,":[67],"compartment":[69],"editor":[70],"complex":[72],"box":[74,81],"start":[75],"configurations,":[76],"interactive":[77],"flexible":[79],"views":[82],"including":[83],"analytics,":[84],"movie":[86],"generation":[87],"or":[88],"animated":[89],"diagrams.":[90],"As":[91],"project,":[94],"allows":[96],"customized":[98],"extensions":[99],"different":[101],"fields":[102],"research.":[104]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
