{"id":"https://openalex.org/W2952811294","doi":"https://doi.org/10.12688/f1000research.17456.1","title":"pdb-tools: a swiss army knife for molecular structures","display_name":"pdb-tools: a swiss army knife for molecular structures","publication_year":2018,"publication_date":"2018-12-20","ids":{"openalex":"https://openalex.org/W2952811294","doi":"https://doi.org/10.12688/f1000research.17456.1","mag":"2952811294","pmid":"https://pubmed.ncbi.nlm.nih.gov/30705752"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.17456.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.17456.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/19090/d71bab65-3e63-4cdb-a677-66af834ed14f_17456_-_joao_rodrigues.pdf?doi=10.12688/f1000research.17456.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/19090/d71bab65-3e63-4cdb-a677-66af834ed14f_17456_-_joao_rodrigues.pdf?doi=10.12688/f1000research.17456.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044499597","display_name":"Jo\u00e3o Rodrigues","orcid":"https://orcid.org/0000-0001-9796-3193"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o P. G. L. M. Rodrigues","raw_affiliation_strings":["Structural Biology, Stanford University School of Medicine, Stanford, California, 94305, USA","Structural Biology, Stanford University School of Medicine, Stanford, California, 94305"],"raw_orcid":"https://orcid.org/0000-0001-9796-3193","affiliations":[{"raw_affiliation_string":"Structural Biology, Stanford University School of Medicine, Stanford, California, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Structural Biology, Stanford University School of Medicine, Stanford, California, 94305","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052389219","display_name":"Jo\u00e3o M. C. Teixeira","orcid":"https://orcid.org/0000-0002-9113-0622"},"institutions":[{"id":"https://openalex.org/I184999862","display_name":"Universidad de Salamanca","ror":"https://ror.org/02f40zc51","country_code":"ES","type":"education","lineage":["https://openalex.org/I184999862"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o M.C. Teixeira","raw_affiliation_strings":["Independent Researcher, Salamanca, Spain","Independent Researcher, Salamanca"],"raw_orcid":"https://orcid.org/0000-0002-9113-0622","affiliations":[{"raw_affiliation_string":"Independent Researcher, Salamanca, Spain","institution_ids":["https://openalex.org/I184999862"]},{"raw_affiliation_string":"Independent Researcher, Salamanca","institution_ids":["https://openalex.org/I184999862"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046643239","display_name":"Mika\u00ebl Trellet","orcid":"https://orcid.org/0000-0001-6337-581X"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mika\u00ebl Trellet","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands","Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]},{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Alexandre M. J. J. Bonvin","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands","Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH"],"raw_orcid":"https://orcid.org/0000-0001-7369-1322","affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]},{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":1.9792,"has_fulltext":false,"cited_by_count":172,"citation_normalized_percentile":{"value":0.87558218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"7","issue":null,"first_page":"1961","last_page":"1961"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9955000281333923,"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":0.9884999990463257,"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/open-peer-review","display_name":"Open peer review","score":0.7517952919006348},{"id":"https://openalex.org/keywords/plant-biology","display_name":"Plant biology","score":0.6590709686279297},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5780985951423645},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.44167301058769226},{"id":"https://openalex.org/keywords/physiology","display_name":"Physiology","score":0.4403616189956665},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4016195237636566},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3990171253681183},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3704882562160492},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3205638825893402},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08367887139320374},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.04142403602600098}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.7517952919006348},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.6590709686279297},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5780985951423645},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.44167301058769226},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.4403616189956665},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4016195237636566},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3990171253681183},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3704882562160492},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3205638825893402},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08367887139320374},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.04142403602600098}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.12688/f1000research.17456.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.17456.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/19090/d71bab65-3e63-4cdb-a677-66af834ed14f_17456_-_joao_rodrigues.pdf?doi=10.12688/f1000research.17456.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"pmid:30705752","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30705752","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":"F1000Research","raw_type":null},{"id":"pmh:oai:doaj.org/article:c0deeab074e64b42a60af7f00842dc19","is_oa":true,"landing_page_url":"https://doaj.org/article/c0deeab074e64b42a60af7f00842dc19","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":"F1000Research, Vol 7 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5331485","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6343223","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/380982","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/380982","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"F1000Research, 2018(7). F1000 Research Ltd.","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.17456.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.17456.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/19090/d71bab65-3e63-4cdb-a677-66af834ed14f_17456_-_joao_rodrigues.pdf?doi=10.12688/f1000research.17456.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7027173739","display_name":null,"funder_award_id":"675728","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"},{"id":"https://openalex.org/G703879418","display_name":null,"funder_award_id":"R35GM122543","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952811294.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1537929670","https://openalex.org/W2029667189","https://openalex.org/W2113904137","https://openalex.org/W2114850508","https://openalex.org/W2123681603","https://openalex.org/W2154019529","https://openalex.org/W2422129218","https://openalex.org/W2898210859"],"related_works":["https://openalex.org/W2248904208","https://openalex.org/W2240080159","https://openalex.org/W2624797522","https://openalex.org/W2247484637","https://openalex.org/W2078218631","https://openalex.org/W2061128535","https://openalex.org/W2734166346","https://openalex.org/W2100707893","https://openalex.org/W4391486731","https://openalex.org/W2219548690"],"abstract_inverted_index":{"The":[0,40],"pdb-tools":[1,41],"are":[2,42,51],"a":[3,35],"collection":[4],"of":[5],"Python":[6],"scripts":[7],"for":[8],"working":[9],"with":[10],"molecular":[11],"structure":[12],"data":[13],"in":[14,34,44],"the":[15,32,55],"Protein":[16],"Data":[17],"Bank":[18],"(PDB)":[19],"format.":[20],"They":[21],"allow":[22],"users":[23],"to":[24],"edit,":[25],"convert,":[26],"and":[27,50,61],"validate":[28],"PDB":[29],"files,":[30],"from":[31],"command-line,":[33],"simple":[36],"but":[37],"efficient":[38],"manner.":[39],"implemented":[43],"Python,":[45],"without":[46],"any":[47],"external":[48],"dependencies,":[49],"freely":[52],"available":[53],"under":[54],"open-source":[56],"Apache":[57],"License":[58],"at":[59],"https://github.com/haddocking/pdb-tools/":[60],"on":[62],"PyPI.":[63]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":31},{"year":2024,"cited_by_count":35},{"year":2023,"cited_by_count":26},{"year":2022,"cited_by_count":41},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}
