{"id":"https://openalex.org/W4386636681","doi":"https://doi.org/10.1186/s13321-023-00748-2","title":"pyPept: a python library to generate atomistic 2D and 3D representations of peptides","display_name":"pyPept: a python library to generate atomistic 2D and 3D representations of peptides","publication_year":2023,"publication_date":"2023-09-12","ids":{"openalex":"https://openalex.org/W4386636681","doi":"https://doi.org/10.1186/s13321-023-00748-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/37700347"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00748-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00748-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00748-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00748-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041873604","display_name":"Rodrigo Ochoa","orcid":"https://orcid.org/0000-0003-0734-2196"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Rodrigo Ochoa","raw_affiliation_strings":["Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany"],"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany","institution_ids":["https://openalex.org/I1330995197"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031474134","display_name":"J. Brown","orcid":"https://orcid.org/0000-0002-4637-1531"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J. B. Brown","raw_affiliation_strings":["Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany"],"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany","institution_ids":["https://openalex.org/I1330995197"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011361588","display_name":"Thomas Fox","orcid":"https://orcid.org/0000-0002-1054-4701"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Fox","raw_affiliation_strings":["Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany. thomas.fox@boehringer-ingelheim.com","Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany"],"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany. thomas.fox@boehringer-ingelheim.com","institution_ids":["https://openalex.org/I1330995197"]},{"raw_affiliation_string":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany","institution_ids":["https://openalex.org/I1330995197"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041873604"],"corresponding_institution_ids":["https://openalex.org/I1330995197"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.8063,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.85280215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"79","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9965000152587891,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9965000152587891,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9945999979972839,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8586629629135132},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.649640679359436},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45923078060150146},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4054710268974304},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24663129448890686}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8586629629135132},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.649640679359436},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45923078060150146},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4054710268974304},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24663129448890686}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00748-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00748-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00748-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:37700347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37700347","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10498622","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10498622","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10498622/pdf/13321_2023_Article_748.pdf","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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:7baa9b5371844f0ca4f95879821ba74b","is_oa":true,"landing_page_url":"https://doaj.org/article/7baa9b5371844f0ca4f95879821ba74b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-10 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00748-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00748-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00748-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310441","display_name":"Boehringer Ingelheim","ror":"https://ror.org/00q32j219"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386636681.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1997379747","https://openalex.org/W2018661561","https://openalex.org/W2034265369","https://openalex.org/W2043338013","https://openalex.org/W2066142272","https://openalex.org/W2072953968","https://openalex.org/W2083224653","https://openalex.org/W2114850508","https://openalex.org/W2141920771","https://openalex.org/W2153594105","https://openalex.org/W2213165966","https://openalex.org/W2244785476","https://openalex.org/W2611907395","https://openalex.org/W2768968558","https://openalex.org/W2796531554","https://openalex.org/W2797220725","https://openalex.org/W2941112903","https://openalex.org/W2952059807","https://openalex.org/W2981018396","https://openalex.org/W3011894284","https://openalex.org/W3014094886","https://openalex.org/W3023697740","https://openalex.org/W3127297964","https://openalex.org/W3137444090","https://openalex.org/W3138308373","https://openalex.org/W3177828909","https://openalex.org/W4292361108","https://openalex.org/W4317867555"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380"],"abstract_inverted_index":{"We":[0],"present":[1],"pyPept,":[2,107],"a":[3,49,59,64,86,109,127],"set":[4],"of":[5,32,73,121,126],"executables":[6],"and":[7,15,76,108,119,123,135,159,163],"underlying":[8],"python-language":[9],"classes":[10],"to":[11,47,88,115],"easily":[12],"create,":[13],"manipulate,":[14],"analyze":[16],"peptide":[17,60,92,128],"molecules":[18],"using":[19],"the":[20,30,71,102,117,131],"FASTA,":[21],"HELM,":[22],"or":[23,80,104,142],"recently-developed":[24],"BILN":[25,136],"notations.":[26],"The":[27,83,161],"framework":[28,162],"enables":[29],"analysis":[31],"both":[33],"pure":[34],"proteinogenic":[35],"peptides":[36,144],"as":[37,39],"well":[38],"those":[40],"with":[41,172],"non-natural":[42],"amino":[43],"acids,":[44],"including":[45],"support":[46],"assemble":[48],"customizable":[50],"monomer":[51],"library,":[52],"without":[53],"requiring":[54],"programming.":[55],"From":[56],"line":[57,132],"notations,":[58],"is":[61,112],"transformed":[62],"into":[63],"molecular":[65],"graph":[66],"for":[67],"2D":[68,122],"depiction":[69],"tasks,":[70],"calculation":[72],"physicochemical":[74],"properties,":[75],"other":[77],"systematic":[78],"analyses":[79],"processing":[81],"pipelines.":[82],"package":[84],"includes":[85],"module":[87],"rapidly":[89],"generate":[90],"approximate":[91],"conformers":[93],"by":[94,101],"incorporating":[95],"secondary":[96],"structure":[97,151],"restraints":[98],"either":[99],"given":[100],"user":[103],"predicted":[105],"via":[106],"wrapper":[110],"tool":[111],"also":[113],"provided":[114],"automate":[116],"generation":[118],"output":[120],"3D":[124],"representations":[125],"directly":[129],"from":[130],"notation.":[133],"HELM":[134],"notations":[137],"that":[138,153],"include":[139],"circular,":[140],"branched,":[141],"stapled":[143],"are":[145,154,169],"fully":[146],"supported,":[147],"eliminating":[148],"errors":[149],"in":[150,167],"creation":[152],"prone":[155],"during":[156],"manual":[157],"drawing":[158],"connecting.":[160],"common":[164],"workflows":[165],"followed":[166],"pyPept":[168,175],"described":[170],"together":[171],"illustrative":[173],"examples.":[174],"has":[176],"been":[177],"released":[178],"at:":[179],"https://github.com/Boehringer-Ingelheim/pyPept":[180],".":[181]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}