{"id":"https://openalex.org/W2493185170","doi":"https://doi.org/10.1186/s12918-016-0294-z","title":"Extending rule-based methods to model molecular geometry and 3D model resolution","display_name":"Extending rule-based methods to model molecular geometry and 3D model resolution","publication_year":2016,"publication_date":"2016-08-01","ids":{"openalex":"https://openalex.org/W2493185170","doi":"https://doi.org/10.1186/s12918-016-0294-z","mag":"2493185170","pmid":"https://pubmed.ncbi.nlm.nih.gov/27490268"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0294-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0294-z","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0294-z","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0294-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054293772","display_name":"Brittany R. Hoard","orcid":"https://orcid.org/0000-0002-1897-1388"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brittany Hoard","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","Department of Computer Science, University of New Mexico, Albuquerque, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024549284","display_name":"Bruna Jacobson","orcid":"https://orcid.org/0000-0001-7718-9794"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruna Jacobson","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","Department of Computer Science, University of New Mexico, Albuquerque, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079697685","display_name":"Kasra Manavi","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kasra Manavi","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","Department of Computer Science, University of New Mexico, Albuquerque, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060753774","display_name":"Lydia Tapia","orcid":"https://orcid.org/0000-0002-7822-7091"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lydia Tapia","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA. tapia@cs.unm.edu","Department of Computer Science, University of New Mexico, Albuquerque, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, 87131, New Mexico, USA. tapia@cs.unm.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5060753774"],"corresponding_institution_ids":["https://openalex.org/I169521973"],"apc_list":null,"apc_paid":null,"fwci":4.7158,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.95305548,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"S2","first_page":"48","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11704","display_name":"Mobile Crowdsensing and Crowdsourcing","score":0.9824000000953674,"subfield":{"id":"https://openalex.org/subfields/1706","display_name":"Computer Science Applications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer 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":0.6029037237167358},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.5528035163879395},{"id":"https://openalex.org/keywords/curvature","display_name":"Curvature","score":0.5445913672447205},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.5021853446960449},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4503839313983917},{"id":"https://openalex.org/keywords/computational-geometry","display_name":"Computational geometry","score":0.4372228980064392},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4229726493358612},{"id":"https://openalex.org/keywords/molecular-model","display_name":"Molecular model","score":0.4184318780899048},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2171143889427185},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17315146327018738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6029037237167358},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.5528035163879395},{"id":"https://openalex.org/C195065555","wikidata":"https://www.wikidata.org/wiki/Q214881","display_name":"Curvature","level":2,"score":0.5445913672447205},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.5021853446960449},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4503839313983917},{"id":"https://openalex.org/C29123130","wikidata":"https://www.wikidata.org/wiki/Q874709","display_name":"Computational geometry","level":2,"score":0.4372228980064392},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4229726493358612},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.4184318780899048},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2171143889427185},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17315146327018738},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0294-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0294-z","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0294-z","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:27490268","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27490268","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4977479","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4977479","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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0294-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0294-z","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0294-z","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1234708948","display_name":null,"funder_award_id":"5P50GM085273","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1332508676","display_name":null,"funder_award_id":"P50GM085273","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G175260837","display_name":null,"funder_award_id":"P20RR018754","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3029198525","display_name":null,"funder_award_id":"P50GM085","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310632","display_name":"Center for Evolutionary and Theoretical Immunology","ror":"https://ror.org/05fs6jp91"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2493185170.pdf","grobid_xml":"https://content.openalex.org/works/W2493185170.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W137961148","https://openalex.org/W1499429477","https://openalex.org/W1563071114","https://openalex.org/W1832276623","https://openalex.org/W1964603087","https://openalex.org/W1969112250","https://openalex.org/W1973846182","https://openalex.org/W1986649132","https://openalex.org/W1987922325","https://openalex.org/W1994344551","https://openalex.org/W2023568310","https://openalex.org/W2034492556","https://openalex.org/W2045598937","https://openalex.org/W2047331390","https://openalex.org/W2052558212","https://openalex.org/W2059654443","https://openalex.org/W2061279689","https://openalex.org/W2073338313","https://openalex.org/W2079704365","https://openalex.org/W2082221311","https://openalex.org/W2086376468","https://openalex.org/W2086928685","https://openalex.org/W2099015579","https://openalex.org/W2118649335","https://openalex.org/W2119232644","https://openalex.org/W2124885315","https://openalex.org/W2125842347","https://openalex.org/W2146099270","https://openalex.org/W2149362274","https://openalex.org/W2163493106","https://openalex.org/W2165700291","https://openalex.org/W2165714871","https://openalex.org/W2168518560","https://openalex.org/W2220901378","https://openalex.org/W2315703236","https://openalex.org/W2381451619","https://openalex.org/W3098157440","https://openalex.org/W4205740352","https://openalex.org/W4313333784"],"related_works":["https://openalex.org/W55883722","https://openalex.org/W2394379345","https://openalex.org/W2079726820","https://openalex.org/W2393870460","https://openalex.org/W3215763795","https://openalex.org/W4288816678","https://openalex.org/W4284894156","https://openalex.org/W2161803855","https://openalex.org/W2118352149","https://openalex.org/W2380616566"],"abstract_inverted_index":{"We":[0],"find":[1],"that":[2,20,36],"the":[3,10,18,31],"optimized":[4,28],"rule-based":[5],"models":[6,29],"provide":[7],"information":[8],"about":[9],"average":[11],"steric":[12],"hindrance":[13],"between":[14],"binding":[15],"regions":[16],"and":[17,43],"probability":[19],"antibodies":[21],"will":[22],"bind":[23],"to":[24],"these":[25],"regions.":[26],"These":[27],"quantify":[30],"variation":[32],"in":[33,40],"aggregate":[34],"size":[35],"results":[37],"from":[38,44],"differences":[39],"molecular":[41],"geometry":[42],"model":[45],"resolution.":[46]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
