{"id":"https://openalex.org/W2949584959","doi":"https://doi.org/10.1093/bioinformatics/bty487","title":"mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling","display_name":"mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling","publication_year":2018,"publication_date":"2018-06-13","ids":{"openalex":"https://openalex.org/W2949584959","doi":"https://doi.org/10.1093/bioinformatics/bty487","mag":"2949584959","pmid":"https://pubmed.ncbi.nlm.nih.gov/29931043"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3948/29153597/bty487.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/34/22/3948/29153597/bty487.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066026197","display_name":"Joseph Masison","orcid":"https://orcid.org/0000-0003-2113-9282"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Masison","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"],"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042482638","display_name":"Paul J. Michalski","orcid":"https://orcid.org/0009-0003-8836-3454"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul J Michalski","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"],"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019048997","display_name":"Leslie M. Loew","orcid":"https://orcid.org/0000-0002-1851-4646"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leslie M Loew","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"],"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012731226","display_name":"Adam D. Schuyler","orcid":"https://orcid.org/0000-0001-7583-899X"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"funder","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam D Schuyler","raw_affiliation_strings":["Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA","institution_ids":["https://openalex.org/I75929689"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5012731226"],"corresponding_institution_ids":["https://openalex.org/I75929689"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2758,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58039011,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"34","issue":"22","first_page":"3948","last_page":"3950"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9901000261306763,"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":0.9901000261306763,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9632999897003174,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9541000127792358,"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/visualization","display_name":"Visualization","score":0.7189001441001892},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.664570689201355},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.6094222068786621},{"id":"https://openalex.org/keywords/domain-decomposition-methods","display_name":"Domain decomposition methods","score":0.5633457899093628},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5532490611076355},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4026125371456146},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.39685726165771484},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3241223692893982},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21884766221046448},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1420820951461792},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11363986134529114},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.0546967089176178}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7189001441001892},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.664570689201355},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.6094222068786621},{"id":"https://openalex.org/C198880260","wikidata":"https://www.wikidata.org/wiki/Q5289813","display_name":"Domain decomposition methods","level":3,"score":0.5633457899093628},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5532490611076355},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4026125371456146},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.39685726165771484},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3241223692893982},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21884766221046448},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1420820951461792},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11363986134529114},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0546967089176178},{"id":"https://openalex.org/C135628077","wikidata":"https://www.wikidata.org/wiki/Q220184","display_name":"Finite element method","level":2,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3948/29153597/bty487.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:29931043","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29931043","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},{"id":"pmh:oai:pubmedcentral.nih.gov:6658811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6658811","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3948/29153597/bty487.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":[],"awards":[{"id":"https://openalex.org/G3030034556","display_name":null,"funder_award_id":"P41 GM103313","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3232485578","display_name":null,"funder_award_id":"P41 GM111135","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320317690","display_name":"University of Connecticut Health Center","ror":"https://ror.org/02kzs4y22"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949584959.pdf","grobid_xml":"https://content.openalex.org/works/W2949584959.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1974035453","https://openalex.org/W1981264193","https://openalex.org/W2054172043","https://openalex.org/W2093795463","https://openalex.org/W2142694980","https://openalex.org/W2271421556","https://openalex.org/W2608193358"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2156434174","https://openalex.org/W2597266923","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2392036275","https://openalex.org/W2044758662"],"abstract_inverted_index":{"https://nmrbox.org/registry/mol2sphere.":[0],"SpringSaLaD":[1,6],"executables":[2],"and":[3],"documentation:":[4],"http://vcell.org/ssalad,":[5],"v.2":[7],"source:":[8],"https://github.com/jmasison/SpringSaLaD.":[9]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}