{"id":"https://openalex.org/W95014119","doi":"https://doi.org/10.1007/978-1-60327-058-8_8","title":"Protein Structure Modeling with MODELLER","display_name":"Protein Structure Modeling with MODELLER","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W95014119","doi":"https://doi.org/10.1007/978-1-60327-058-8_8","mag":"95014119","pmid":"https://pubmed.ncbi.nlm.nih.gov/18542861"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-60327-058-8_8","doi":"https://doi.org/10.1007/978-1-60327-058-8_8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-60327-058-8_8","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W2399364539","display_name":"Structural Proteomics"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032919166","display_name":"Narayanan Eswar","orcid":"https://orcid.org/0009-0000-3711-2821","observed_orcids":["https://orcid.org/0009-0000-3711-2821"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Narayanan Eswar","raw_affiliation_strings":["Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA, USA","Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044756888","display_name":"David Eramian","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Eramian","raw_affiliation_strings":["Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010129208","display_name":"Benjamin Webb","orcid":"https://orcid.org/0000-0003-3360-4540","observed_orcids":["https://orcid.org/0000-0003-3360-4540"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Webb","raw_affiliation_strings":["Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110116750","display_name":"Min\u2010Yi Shen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Min-Yi Shen","raw_affiliation_strings":["Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028845140","display_name":"Andrej \u0160ali","orcid":"https://orcid.org/0000-0003-0435-6197","observed_orcids":["https://orcid.org/0000-0003-0435-6197"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrej Sali","raw_affiliation_strings":["Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, California","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":null,"apc_paid":null,"fwci":79.4617,"has_fulltext":false,"cited_by_count":1786,"citation_normalized_percentile":{"value":0.99985367,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"426","issue":null,"first_page":"145","last_page":"159"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9897000193595886,"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":0.9897000193595886,"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/T11162","display_name":"Enzyme Structure and Function","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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/protein-structure-modeling","display_name":"protein structure modeling","score":0.925000011920929},{"id":"https://openalex.org/keywords/modeller","display_name":"MODELLER","score":0.9660000205039978},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"homology modeling","score":0.8980000019073486},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.7730000019073486},{"id":"https://openalex.org/keywords/protein-domains","display_name":"protein domains","score":0.6340000033378601}],"concepts":[{"id":"https://openalex.org/C193153401","wikidata":"https://www.wikidata.org/wiki/Q3859815","display_name":"MODELLER","level":4,"score":0.9833476543426514},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6041167974472046},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5500921607017517},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.48606064915657043},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4765373170375824},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4531926214694977},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.42123234272003174},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.4016364812850952},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32572096586227417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27873802185058594},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19262075424194336},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13891175389289856},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08861121535301208},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/978-1-60327-058-8_8","doi":"https://doi.org/10.1007/978-1-60327-058-8_8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-60327-058-8_8","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},{"id":"pmid:18542861","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18542861","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,"listed_in":[],"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":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1107471347","display_name":"IMP: Software for Hybrid Determination of Macromolecular Assembly Structures","funder_award_id":"R01GM083960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1528331171","https://openalex.org/W1971149989","https://openalex.org/W1972436355","https://openalex.org/W1980374511","https://openalex.org/W1989415425","https://openalex.org/W1991540499","https://openalex.org/W1999613945","https://openalex.org/W2002992883","https://openalex.org/W2004228538","https://openalex.org/W2027408247","https://openalex.org/W2034100527","https://openalex.org/W2042992947","https://openalex.org/W2051831487","https://openalex.org/W2051969447","https://openalex.org/W2052112948","https://openalex.org/W2053449148","https://openalex.org/W2054211501","https://openalex.org/W2059324948","https://openalex.org/W2065283382","https://openalex.org/W2074231493","https://openalex.org/W2080022084","https://openalex.org/W2087064593","https://openalex.org/W2087254300","https://openalex.org/W2101220662","https://openalex.org/W2103159791","https://openalex.org/W2103273582","https://openalex.org/W2105801262","https://openalex.org/W2108376320","https://openalex.org/W2109402847","https://openalex.org/W2114520383","https://openalex.org/W2115213105","https://openalex.org/W2125898812","https://openalex.org/W2128484254","https://openalex.org/W2129153475","https://openalex.org/W2130479394","https://openalex.org/W2131724426","https://openalex.org/W2131736388","https://openalex.org/W2132262459","https://openalex.org/W2137604324","https://openalex.org/W2143210482","https://openalex.org/W2144357990","https://openalex.org/W2146134187","https://openalex.org/W2147059525","https://openalex.org/W2150399099","https://openalex.org/W2156328030","https://openalex.org/W2158714788","https://openalex.org/W2162751934","https://openalex.org/W2163312887","https://openalex.org/W2166458835","https://openalex.org/W2170471837","https://openalex.org/W2887067015","https://openalex.org/W4230842383"],"related_works":["https://openalex.org/W7097392571","https://openalex.org/W1528331171","https://openalex.org/W1543174845","https://openalex.org/W4211156111","https://openalex.org/W12382117","https://openalex.org/W3118902215","https://openalex.org/W2055878484","https://openalex.org/W253094825","https://openalex.org/W2142585587","https://openalex.org/W2051831487"],"abstract_inverted_index":{"Genome":[0],"sequencing":[1],"projects":[2],"have":[3,24,37],"resulted":[4,75],"in":[5,9,76,83],"a":[6,58,62],"rapid":[7],"increase":[8],"the":[10,38,52],"number":[11],"of":[12,21,54,68,72,78,87],"known":[13,89],"protein":[14,33,63,90],"sequences.":[15,91],"In":[16],"contrast,":[17],"only":[18],"about":[19],"one-hundredth":[20],"these":[22],"sequences":[23],"been":[25],"characterized":[26],"using":[27],"experimental":[28],"structure":[29,34],"determination":[30],"methods.":[31],"Computational":[32],"modeling":[35],"techniques":[36],"potential":[39],"to":[40,56],"bridge":[41],"this":[42],"sequence-structure":[43],"gap.":[44],"This":[45],"chapter":[46],"presents":[47],"an":[48],"example":[49],"that":[50],"illustrates":[51],"use":[53],"MODELLER":[55],"construct":[57],"comparative":[59],"model":[60],"for":[61,81],"with":[64],"unknown":[65],"structure.":[66],"Automation":[67],"similar":[69],"protocols":[70],"(correction":[71],"protcols)":[73],"has":[74],"models":[77],"useful":[79],"accuracy":[80],"domains":[82],"more":[84],"than":[85],"half":[86],"all":[88]},"counts_by_year":[{"year":2026,"cited_by_count":18},{"year":2025,"cited_by_count":43},{"year":2024,"cited_by_count":73},{"year":2023,"cited_by_count":103},{"year":2022,"cited_by_count":111},{"year":2021,"cited_by_count":128},{"year":2020,"cited_by_count":183},{"year":2019,"cited_by_count":166},{"year":2018,"cited_by_count":179},{"year":2017,"cited_by_count":124},{"year":2016,"cited_by_count":105},{"year":2015,"cited_by_count":93},{"year":2014,"cited_by_count":114},{"year":2013,"cited_by_count":87},{"year":2012,"cited_by_count":75}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
