{"id":"https://openalex.org/W2950428171","doi":"https://doi.org/10.1093/bioinformatics/bty077","title":"ssbio: a Python framework for structural systems biology","display_name":"ssbio: a Python framework for structural systems biology","publication_year":2018,"publication_date":"2018-02-09","ids":{"openalex":"https://openalex.org/W2950428171","doi":"https://doi.org/10.1093/bioinformatics/bty077","mag":"2950428171","pmid":"https://pubmed.ncbi.nlm.nih.gov/29444205"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/12/2155/29153549/bty077.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/34/12/2155/29153549/bty077.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023323263","display_name":"Nathan Mih","orcid":"https://orcid.org/0000-0002-4302-9052"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nathan Mih","raw_affiliation_strings":["Department of Bioengineering, Bioinformatics and Systems Biology Graduate Program","Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Bioinformatics and Systems Biology Graduate Program","institution_ids":[]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002596498","display_name":"Elizabeth Brunk","orcid":"https://orcid.org/0000-0001-8578-8658"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth Brunk","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100451980","display_name":"Ke Chen","orcid":"https://orcid.org/0000-0001-8357-3741"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ke Chen","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020518995","display_name":"Edward Catoiu","orcid":"https://orcid.org/0000-0001-8680-7291"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Catoiu","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047222181","display_name":"Anand V. Sastry","orcid":"https://orcid.org/0000-0002-8293-3909"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anand Sastry","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053271048","display_name":"Erol Kavvas","orcid":"https://orcid.org/0000-0003-2525-0818"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erol Kavvas","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088968927","display_name":"Jonathan M. Monk","orcid":"https://orcid.org/0000-0002-3895-8949"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan M Monk","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390211","display_name":"Zhen Zhang","orcid":"https://orcid.org/0000-0003-4657-0589"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Zhang","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernhard O Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5023323263"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.39,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.89949895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"12","first_page":"2155","last_page":"2157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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":0.9987000226974487,"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/python","display_name":"Python (programming language)","score":0.8902381658554077},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.8340858221054077},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7335429787635803},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6456044912338257},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6108794808387756},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.473347932100296},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3824925422668457},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.34555092453956604},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1870189905166626}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8902381658554077},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.8340858221054077},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7335429787635803},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6456044912338257},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6108794808387756},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.473347932100296},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3824925422668457},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.34555092453956604},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1870189905166626}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D011487","descriptor_name":"Protein 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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/12/2155/29153549/bty077.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:29444205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29444205","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:escholarship.org:ark:/13030/qt1f12k2bw","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1f12k2bw","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 34, iss 12","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6658713","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6658713","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/bty077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/12/2155/29153549/bty077.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/G5700171112","display_name":null,"funder_award_id":"p2elp2_148961","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G6501738669","display_name":null,"funder_award_id":"1-U01-AI124316-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7955033520","display_name":null,"funder_award_id":"U01-GM102098","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950428171.pdf","grobid_xml":"https://content.openalex.org/works/W2950428171.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1665355332","https://openalex.org/W1986111357","https://openalex.org/W1989061197","https://openalex.org/W1991004166","https://openalex.org/W2008708467","https://openalex.org/W2019974881","https://openalex.org/W2037312364","https://openalex.org/W2043359500","https://openalex.org/W2048465561","https://openalex.org/W2053448121","https://openalex.org/W2069152576","https://openalex.org/W2081231176","https://openalex.org/W2096495474","https://openalex.org/W2114850508","https://openalex.org/W2119228200","https://openalex.org/W2139300598","https://openalex.org/W2148044817","https://openalex.org/W2153921000","https://openalex.org/W2168172687","https://openalex.org/W2170243504","https://openalex.org/W2293705795","https://openalex.org/W2419335772","https://openalex.org/W2500151731","https://openalex.org/W2522753993","https://openalex.org/W2557679158","https://openalex.org/W2760895823","https://openalex.org/W2764202526","https://openalex.org/W2772099288","https://openalex.org/W4246407778","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4287775886","https://openalex.org/W2748802065","https://openalex.org/W4225687299"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}