{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T03:58:56Z","timestamp":1771732736725,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"MCIN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Czech Ministry of Education"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes modules for macromolecular interactions, loops, super-secondary structures, and biological sequences, as well as wrappers for external tools with which to integrate their results and facilitate the comparative analysis of protein structures and their complexes. The library can handle macromolecular complexes formed by proteins and\/or nucleic acid molecules (i.e. DNA and RNA). It is uniquely capable of parsing and calculating protein super-secondary structure and loop geometry. We have compiled a list of example scenarios which SBILib may be applied to and provided access to these within the library.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SBILib is made available on Github at https:\/\/github.com\/structuralbioinformatics\/SBILib.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad613","type":"journal-article","created":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T17:29:31Z","timestamp":1696526971000},"source":"Crossref","is-referenced-by-count":5,"title":["SBILib: a handle for protein modeling and engineering"],"prefix":"10.1093","volume":"39","author":[{"given":"Patrick","family":"Gohl","sequence":"first","affiliation":[{"name":"Department of Medicine and Life Sciences, SBI-GRIB, Universitat Pompeu Fabra , 08003 Barcelona, Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5210-4387","authenticated-orcid":false,"given":"Jaume","family":"Bonet","sequence":"additional","affiliation":[{"name":"Department of Medicine and Life Sciences, SBI-GRIB, Universitat Pompeu Fabra , 08003 Barcelona, Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5969-3054","authenticated-orcid":false,"given":"Oriol","family":"Fornes","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children\u2019s Hospital Research Institute, University of British Columbia , Vancouver, BC V5Z 4H4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6279-2483","authenticated-orcid":false,"given":"Joan","family":"Planas-Iglesias","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"International Clinical Research Center, St Anne\u2019s University Hospital Brno , 656 916 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6421-1080","authenticated-orcid":false,"given":"Narc\u00eds","family":"Fernandez-Fuentes","sequence":"additional","affiliation":[{"name":"Institute of Biological, Environmental and Rural Science, Aberystwyth University , Aberystwyth SY23 3DA, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0702-0250","authenticated-orcid":false,"given":"Baldo","family":"Oliva","sequence":"additional","affiliation":[{"name":"Department of Medicine and Life Sciences, SBI-GRIB, Universitat Pompeu Fabra , 08003 Barcelona, Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,10,5]]},"reference":[{"key":"2023102111031719500_btad613-B1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s12859-020-03770-5","article-title":"SPServer: split-statistical potentials for the analysis of protein structures and protein\u2013protein interactions","volume":"22","author":"Aguirre-Plans","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2023102111031719500_btad613-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023102111031719500_btad613-B3","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkt1189","article-title":"ArchDB 2014: structural classification of loops in proteins","volume":"42","author":"Bonet","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023102111031719500_btad613-B4","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1093\/bioinformatics\/btu129","article-title":"Frag\u2019r\u2019Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design","volume":"30","author":"Bonet","year":"2014","journal-title":"Bioinformatics"},{"key":"2023102111031719500_btad613-B5","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023102111031719500_btad613-B6","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023102111031719500_btad613-B7","author":"Eswar"},{"key":"2023102111031719500_btad613-B8","doi-asserted-by":"crossref","first-page":"e1000750","DOI":"10.1371\/journal.pcbi.1000750","article-title":"Structural characteristics of novel protein folds","volume":"6","author":"Fernandez-Fuentes","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"2023102111031719500_btad613-B9","doi-asserted-by":"crossref","first-page":"W173","DOI":"10.1093\/nar\/gkl113","article-title":"ArchPRED: a template based loop structure prediction server","volume":"34","author":"Fernandez-Fuentes","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023102111031719500_btad613-B10","author":"Fornes","year":"2022"},{"key":"2023102111031719500_btad613-B11","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023102111031719500_btad613-B12","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2023102111031719500_btad613-B13","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1093\/bioinformatics\/btaa072","article-title":"Atomium\u2014a python structure parser","volume":"36","author":"Ireland","year":"2020","journal-title":"Bioinformatics"},{"key":"2023102111031719500_btad613-B14","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/321522a0","article-title":"Replacing the complementarity-determining regions in a human antibody with those from a mouse","volume":"321","author":"Jones","year":"1986","journal-title":"Nature"},{"key":"2023102111031719500_btad613-B15","first-page":"2577","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolym Original Res Biomol"},{"key":"2023102111031719500_btad613-B16","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1002\/0471721204.ch25","article-title":"Homology modeling","volume":"44","author":"Krieger","year":"2003","journal-title":"Methods Biochem Anal"},{"key":"2023102111031719500_btad613-B17","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1186\/s12859-023-05345-6","article-title":"Biotite: new tools for a versatile Python bioinformatics library","volume":"24","author":"Kunzmann","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2023102111031719500_btad613-B18","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/protein\/15.8.677","article-title":"A fast empirical approach to binding free energy calculations based on protein interface information","volume":"15","author":"Ma","year":"2002","journal-title":"Protein Eng"},{"key":"2023102111031719500_btad613-B19","doi-asserted-by":"crossref","first-page":"2112","DOI":"10.1002\/pro.3930","article-title":"Using collections of structural models to predict changes of binding affinity caused by mutations in protein\u2013protein interactions","volume":"29","author":"Meseguer","year":"2020","journal-title":"Protein Sci"},{"key":"2023102111031719500_btad613-B20","doi-asserted-by":"crossref","first-page":"166656","DOI":"10.1016\/j.jmb.2020.09.015","article-title":"Galaxy InteractoMIX: an integrated computational platform for the study of protein\u2013protein interaction data","volume":"433","author":"Mirela-Bota","year":"2021","journal-title":"J Mol Biol"},{"key":"2023102111031719500_btad613-B21","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.12688\/f1000research.17456.1","article-title":"pdb-tools: a swiss army knife for molecular structures","volume":"7","author":"Rodrigues","year":"2018","journal-title":"F1000Res"},{"key":"2023102111031719500_btad613-B22","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignments","volume":"12","author":"Rost","year":"1999","journal-title":"Protein Eng"},{"key":"2023102111031719500_btad613-B23","doi-asserted-by":"crossref","first-page":"3616","DOI":"10.1038\/s41467-021-23450-z","article-title":"Engineering the protein dynamics of an ancestral luciferase","volume":"12","author":"Schenkmayerova","year":"2021","journal-title":"Nat Commun"},{"key":"2023102111031719500_btad613-B24","doi-asserted-by":"crossref","first-page":"30486","DOI":"10.1074\/jbc.270.51.30486","article-title":"Protein loop grafting to construct a variant of tissue-type plasminogen activator that binds platelet integrin \u03b1IIb\u03b23 (\u2217)","volume":"270","author":"Smith","year":"1995","journal-title":"J Biol Chem"},{"key":"2023102111031719500_btad613-B25","doi-asserted-by":"crossref","first-page":"18398","DOI":"10.1074\/jbc.RA119.010658","article-title":"Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy","volume":"294","author":"Tang","year":"2019","journal-title":"J Biol Chem"},{"key":"2023102111031719500_btad613-B26","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gku1028","article-title":"A series of PDB-related databanks for everyday needs","volume":"43","author":"Touw","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023102111031719500_btad613-B27","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023102111031719500_btad613-B28","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/s41592-020-0772-5","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"2023102111031719500_btad613-B29","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.jmb.2005.08.020","article-title":"Loss of protein structure stability as a major causative factor in monogenic disease","volume":"353","author":"Yue","year":"2005","journal-title":"J Mol Biol"},{"key":"2023102111031719500_btad613-B30","doi-asserted-by":"crossref","first-page":"3657","DOI":"10.1093\/bioinformatics\/btab187","article-title":"ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python","volume":"37","author":"Zhang","year":"2021","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad613\/51893673\/btad613.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad613\/52327134\/btad613.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad613\/52327134\/btad613.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,21]],"date-time":"2023-10-21T11:04:08Z","timestamp":1697886248000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad613\/7291855"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,10,1]]},"references-count":30,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2023,10,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad613","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,10,1]]},"published":{"date-parts":[[2023,10,1]]},"article-number":"btad613"}}