{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T01:48:29Z","timestamp":1783734509813,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T00:00:00Z","timestamp":1638403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1832184"],"award-info":[{"award-number":["DBI-1832184"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0019749"],"award-info":[{"award-number":["DE-SC0019749"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Cancer Institute, National Institute of Allergy and Infectious Diseases"},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM133198"],"award-info":[{"award-number":["R01GM133198"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by \u223c80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com\/molstar\/molstar).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab813","type":"journal-article","created":{"date-parts":[[2021,11,30]],"date-time":"2021-11-30T04:19:37Z","timestamp":1638245977000},"page":"1452-1454","source":"Crossref","is-referenced-by-count":66,"title":["RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3576-0387","authenticated-orcid":false,"given":"Sebastian","family":"Bittrich","sequence":"first","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yana","family":"Rose","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joan","family":"Segura","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Lowe","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"},{"name":"Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6686-5475","authenticated-orcid":false,"given":"John D","family":"Westbrook","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"},{"name":"Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"},{"name":"Cancer Institute of New Jersey, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9544-5621","authenticated-orcid":false,"given":"Jose M","family":"Duarte","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen K","family":"Burley","sequence":"additional","affiliation":[{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, USA"},{"name":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"},{"name":"Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"},{"name":"Cancer Institute of New Jersey, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901, USA"},{"name":"Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,12,2]]},"reference":[{"key":"2023020108550478800_btab813-B1","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB protein data bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023020108550478800_btab813-B2","doi-asserted-by":"crossref","first-page":"D524","DOI":"10.1093\/nar\/gks1169","article-title":"PDBTM: protein data bank of transmembrane proteins after 8 years","volume":"41","author":"Kozma","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020108550478800_btab813-B3","doi-asserted-by":"crossref","first-page":"D370","DOI":"10.1093\/nar\/gkr703","article-title":"OPM database and ppm web server: resources for positioning of proteins in membranes","volume":"40","author":"Lomize","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020108550478800_btab813-B4","doi-asserted-by":"crossref","first-page":"D390","DOI":"10.1093\/nar\/gky1047","article-title":"The memprotmd database: a resource for membrane-embedded protein structures and their lipid interactions","volume":"47","author":"Newport","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023020108550478800_btab813-B5","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/protein\/gzv063","article-title":"Membrane positioning for high-and low-resolution protein structures through a binary classification approach","volume":"29","author":"Postic","year":"2016","journal-title":"Protein Eng. 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Biol"},{"key":"2023020108550478800_btab813-B7","doi-asserted-by":"crossref","first-page":"5526","DOI":"10.1093\/bioinformatics\/btaa1012","article-title":"RCSB Protein Data Bank 1D tools and services","volume":"36","author":"Segura","year":"2021","journal-title":"Bioinformatics"},{"key":"2023020108550478800_btab813-B8","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol viewer: modern web app for 3d visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023020108550478800_btab813-B9","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/j.bbamem.2018.01.005","article-title":"Comparative analysis of membrane protein structure databases","volume":"1860","author":"Shimizu","year":"2018","journal-title":"Biochim. Biophys. 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