Analysis of impact metrics for the Protein Data Bank

Markosian, Christopher; Di Costanzo, Luigi; Sekharan, Monica; Shao, Chenghua; Burley, Stephen K.; Zardecki, Christine

doi:10.1038/sdata.2018.212

Title: Analysis of impact metrics for the Protein Data Bank

Journal Article · 15 October 2018 · Scientific Data

DOI: https://doi.org/10.1038/sdata.2018.212 · OSTI ID:1624555

Markosian, Christopher ^[1]; Di Costanzo, Luigi ^[2]; Sekharan, Monica ^[2]; Shao, Chenghua ^[2]; Burley, Stephen K. ^[3]; Zardecki, Christine ^[2]

Rutgers Univ., Piscataway, NJ (United States); DOE/OSTI
Rutgers Univ., Piscataway, NJ (United States)
Rutgers Univ., Piscataway, NJ (United States); Univ. of California San Diego, La Jolla, CA (United States)

Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules. The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms. Knowing the 3D structure of a biological macromolecule is essential for understanding the molecule’s function, providing insights in health and disease, food and energy production, and other topics of concern to prosperity and sustainability. PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics. Our analysis shows that even though research areas such as molecular biology and biochemistry account for the most usage, other fields are increasingly using PDB resources. PDB usage is seen across 150 disciplines in applied sciences, humanities, and social sciences. Data are also re-used and integrated with >400 resources. Our study identifies trends in PDB usage and documents its utility across research disciplines.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE

OSTI ID:: 1624555

Journal Information:: Scientific Data, Journal Name: Scientific Data Journal Issue: 1 Vol. 5; ISSN 2052-4463

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (149)

Long noncoding RNA LINC00844-mediated molecular network regulates expression of drug metabolizing enzymes and nuclear receptors in human liver cells Li, Dongying; Wu, Leihong; Knox, Bridgett Archives of Toxicology, Vol. 94, Issue 5 https://doi.org/10.1007/s00204-020-02706-5	journal	March 2020
Adherence to literature search reporting guidelines in leading rheumatology journals’ systematic reviews: umbrella review protocol Pérez-Neri, Iván; Pineda, Carlos; Flores-Guerrero, Jose L. Rheumatology International, Vol. 42, Issue 12 https://doi.org/10.1007/s00296-022-05194-1	journal	August 2022
Evidence for an association of interferon gene variants with sudden infant death syndrome Hafke, Angelina; Schürmann, Peter; Rothämel, Thomas International Journal of Legal Medicine, Vol. 133, Issue 3 https://doi.org/10.1007/s00414-018-1974-6	journal	January 2019
The top 100 papers Van Noorden, Richard; Maher, Brendan; Nuzzo, Regina Nature, Vol. 514, Issue 7524 https://doi.org/10.1038/514550a	journal	October 2014
Metabolite identification via the Madison Metabolomics Consortium Database Cui, Qiu; Lewis, Ian A.; Hegeman, Adrian D. Nature Biotechnology, Vol. 26, Issue 2 https://doi.org/10.1038/nbt0208-162	journal	February 2008
Announcing the worldwide Protein Data Bank Berman, Helen; Henrick, Kim; Nakamura, Haruki Nature Structural & Molecular Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nsb1203-980	journal	December 2003
A novel circular RNA, circIgfbp2, links neural plasticity and anxiety through targeting mitochondrial dysfunction and oxidative stress-induced synapse dysfunction after traumatic brain injury Du, Mengran; Wu, Chenrui; Yu, Renqiang Molecular Psychiatry, Vol. 27, Issue 11 https://doi.org/10.1038/s41380-022-01711-7	journal	August 2022
Utilizing MALDI-TOF MS and LC-MS/MS to access serum peptidome-based biomarkers in canine oral tumors Ploypetch, Sekkarin; Jaresitthikunchai, Janthima; Phaonakrop, Narumon Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-26132-y	journal	December 2022
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Mutation analysis of the entire mitochondrial genome using denaturing high performance liquid chromatography van den Bosch, B. J. C. Nucleic Acids Research, Vol. 28, Issue 20 https://doi.org/10.1093/nar/28.20.e89	journal	October 2000
PIRSF: family classification system at the Protein Information Resource Wu, C. H. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh097	journal	January 2004
VIPERdb: a relational database for structural virology Shepherd, C. M. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj032	journal	January 2006
BioMagResBank Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm957	journal	December 2007
REPAIRtoire--a database of DNA repair pathways Milanowska, K.; Krwawicz, J.; Papaj, G. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1087	journal	November 2010
Saccharomyces Genome Database: the genomics resource of budding yeast Cherry, J. M.; Hong, E. L.; Amundsen, C. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1029	journal	November 2011
MODOMICS: a database of RNA modification pathways—2013 update Machnicka, Magdalena A.; Milanowska, Kaja; Osman Oglou, Okan Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1007	journal	October 2012
EcoCyc: fusing model organism databases with systems biology Keseler, Ingrid M.; Mackie, Amanda; Peralta-Gil, Martin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1027	journal	November 2012
HMDB 3.0—The Human Metabolome Database in 2013 Wishart, David S.; Jewison, Timothy; Guo, An Chi Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1065	journal	November 2012
The ChEMBL bioactivity database: an update Bento, A. Patrícia; Gaulton, Anna; Hersey, Anne Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1031	journal	November 2013
SAbDab: the structural antibody database Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1043	journal	November 2013
TheCandidaGenome Database: The new homology information page highlights protein similarity and phylogeny Binkley, Jonathan; Arnaud, Martha B.; Inglis, Diane O. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1046	journal	October 2013
MultitaskProtDB: a database of multitasking proteins Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1153	journal	November 2013
SCOP2 prototype: a new approach to protein structure mining Andreeva, Antonina; Howorth, Dave; Chothia, Cyrus Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1242	journal	November 2013
PDBsum additions de Beer, Tjaart A. P.; Berka, Karel; Thornton, Janet M. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt940	journal	October 2013
STRING v10: protein–protein interaction networks, integrated over the tree of life Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1003	journal	October 2014
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease Shimoyama, Mary; De Pons, Jeff; Hayman, G. Thomas Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1026	journal	October 2014
IMGT®, the international ImMunoGeneTics information system® 25 years on Lefranc, Marie-Paule; Giudicelli, Véronique; Duroux, Patrice Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1056	journal	November 2014
ArrayExpress update—simplifying data submissions Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1057	journal	October 2014
Rfam 12.0: updates to the RNA families database Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1063	journal	November 2014
Genenames.org: the HGNC resources in 2015 Gray, Kristian A.; Yates, Bethan; Seal, Ruth L. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1071	journal	October 2014
COSMIC: exploring the world's knowledge of somatic mutations in human cancer Forbes, Simon A.; Beare, David; Gunasekaran, Prasad Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1075	journal	October 2014
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1117	journal	December 2014
Cancer3D: understanding cancer mutations through protein structures Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1140	journal	November 2014
CDD: NCBI's conserved domain database Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1221	journal	November 2014
The immune epitope database (IEDB) 3.0 Vita, Randi; Overton, James A.; Greenbaum, Jason A. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku938	journal	October 2014
SMART: recent updates, new developments and status in 2015 Letunic, Ivica; Doerks, Tobias; Bork, Peer Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku949	journal	October 2014
ChEBI in 2016: Improved services and an expanding collection of metabolites Hastings, Janna; Owen, Gareth; Dekker, Adriano Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1031	journal	October 2015
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1047	journal	October 2015
The Transporter Classification Database (TCDB): recent advances Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1103	journal	November 2015
DNA data bank of Japan (DDBJ) progress report Mashima, Jun; Kodama, Yuichi; Kosuge, Takehide Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1105	journal	November 2015
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles Mathelier, Anthony; Fornes, Oriol; Arenillas, David J. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1176	journal	November 2015
GPCRdb: an information system for G protein-coupled receptors Isberg, Vignir; Mordalski, Stefan; Munk, Christian Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1178	journal	November 2015
Ensembl Genomes 2016: more genomes, more complexity Kersey, Paul Julian; Allen, James E.; Armean, Irina Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1209	journal	November 2015
Mouse genome database 2016 Bult, Carol J.; Eppig, Janan T.; Blake, Judith A. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1211	journal	November 2015
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1240	journal	November 2015
TheSaccharomycesGenome Database Variant Viewer Sheppard, Travis K.; Hitz, Benjamin C.; Engel, Stacia R. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1250	journal	November 2015
ELM 2016—data update and new functionality of the eukaryotic linear motif resource Dinkel, Holger; Van Roey, Kim; Michael, Sushama Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1291	journal	November 2015
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
The Reactome pathway Knowledgebase Fabregat, Antonio; Sidiropoulos, Konstantinos; Garapati, Phani Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1351	journal	December 2015
PubChem Substance and Compound databases Kim, Sunghwan; Thiessen, Paul A.; Bolton, Evan E. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv951	journal	September 2015
The SWISS-MODEL Repository—new features and functionality Bienert, Stefan; Waterhouse, Andrew; de Beer, Tjaart A. P. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1132	journal	November 2016
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw962	journal	October 2016
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes Galperin, Michael Y.; Fernández-Suárez, Xosé M.; Rigden, Daniel J. Nucleic Acids Research https://doi.org/10.1093/nar/gkx021	journal	January 2017
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe Mir, Saqib; Alhroub, Younes; Anyango, Stephen Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1070	journal	November 2017
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection Rigden, Daniel J.; Fernández, Xosé M. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1235	journal	December 2017
The Protein Data Bank: a historical perspective Berman, Helen M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/s0108767307035623	journal	December 2007
Response toOn prompt update of literature references in the Protein Data Bank Berman, Helen M.; Burley, Stephen K.; Kleywegt, Gerard J. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10 https://doi.org/10.1107/s1399004714020513	journal	September 2014
Citing a Data Repository: A Case Study of the Protein Data Bank Huang, Yi-Hung; Rose, Peter W.; Hsu, Chun-Nan PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0136631	journal	August 2015
Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank" Basner, Jodi RCSB Protein Data Bank https://doi.org/10.2210/rcsb_pdb/pdb-cit-anal-2017	journal	May 2017
A comparison of two techniques for bibliometric mapping: Multidimensional scaling and VOS van Eck, Nees Jan; Waltman, Ludo; Dekker, Rommert arXiv https://doi.org/10.48550/arxiv.1003.2551	preprint	January 2010
Analysis of Impact Metrics for the Protein Data Bank Markosian, Christopher; Costanzo, Luigi Di; Sekharan, Monica Figshare https://doi.org/10.6084/m9.figshare.c.4064561	collection	January 2018
A comparison of two techniques for bibliometric mapping: Multidimensional scaling and VOS van Eck, Nees Jan; Waltman, Ludo; Dekker, Rommert Journal of the American Society for Information Science and Technology, Vol. 61, Issue 12 https://doi.org/10.1002/asi.21421	journal	December 2010
Software survey: VOSviewer, a computer program for bibliometric mapping van Eck, Nees Jan; Waltman, Ludo Scientometrics, Vol. 84, Issue 2 https://doi.org/10.1007/s11192-009-0146-3	journal	December 2009
Strategies for design of improved biocatalysts for industrial applications Madhavan, Aravind; Sindhu, Raveendran; Binod, Parameswaran Bioresource Technology, Vol. 245 https://doi.org/10.1016/j.biortech.2017.05.031	journal	December 2017
Antifungal activity of flavonoids from Heteropterys byrsonimifolia and a commercial source against Aspergillus ochraceus: In silico interactions of these compounds with a protein kinase Santos Júnior, Helvécio M.; Campos, Viviane A. C.; Alves, Dejane S. Crop Protection, Vol. 62 https://doi.org/10.1016/j.cropro.2014.04.012	journal	August 2014
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang Structure, Vol. 25, Issue 3 https://doi.org/10.1016/j.str.2017.01.004	journal	March 2017
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank Kellenberger, Esther; Muller, Pascal; Schalon, Claire Journal of Chemical Information and Modeling, Vol. 46, Issue 2 https://doi.org/10.1021/ci050372x	journal	January 2006
The top 100 papers Van Noorden, Richard; Maher, Brendan; Nuzzo, Regina Nature, Vol. 514, Issue 7524 https://doi.org/10.1038/514550a	journal	October 2014
Metabolite identification via the Madison Metabolomics Consortium Database Cui, Qiu; Lewis, Ian A.; Hegeman, Adrian D. Nature Biotechnology, Vol. 26, Issue 2 https://doi.org/10.1038/nbt0208-162	journal	February 2008
Crystallography: Protein Data Bank Skipper, Magdalena Nature New Biology, Vol. 233, Issue 42, p. 223-223 https://doi.org/10.1038/newbio233223b0	journal	October 1971
Announcing the worldwide Protein Data Bank Berman, Helen; Henrick, Kim; Nakamura, Haruki Nature Structural & Molecular Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nsb1203-980	journal	December 2003
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Imaging and the Human Brain Project: A Review Rosse, C.; Brinkley, J. F. Methods of Information in Medicine, Vol. 41, Issue 04 https://doi.org/10.1055/s-0038-1634485	journal	January 2002
The Molecular Biology Database Collection: an online compilation of relevant database resources Baxevanis, A. D. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.1	journal	January 2000
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
PIRSF: family classification system at the Protein Information Resource Wu, C. H. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh097	journal	January 2004
VIPERdb: a relational database for structural virology Shepherd, C. M. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj032	journal	January 2006
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB Block, P. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj039	journal	January 2006
BioMagResBank Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm957	journal	December 2007
REPAIRtoire--a database of DNA repair pathways Milanowska, K.; Krwawicz, J.; Papaj, G. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1087	journal	November 2010
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Kawaji, H.; Severin, J.; Lizio, M. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1112	journal	November 2010
Saccharomyces Genome Database: the genomics resource of budding yeast Cherry, J. M.; Hong, E. L.; Amundsen, C. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1029	journal	November 2011
MODOMICS: a database of RNA modification pathways—2013 update Machnicka, Magdalena A.; Milanowska, Kaja; Osman Oglou, Okan Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1007	journal	October 2012
EcoCyc: fusing model organism databases with systems biology Keseler, Ingrid M.; Mackie, Amanda; Peralta-Gil, Martin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1027	journal	November 2012
HMDB 3.0—The Human Metabolome Database in 2013 Wishart, David S.; Jewison, Timothy; Guo, An Chi Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1065	journal	November 2012
New and continuing developments at PROSITE Sigrist, Christian J. A.; de Castro, Edouard; Cerutti, Lorenzo Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1067	journal	November 2012
The ChEMBL bioactivity database: an update Bento, A. Patrícia; Gaulton, Anna; Hersey, Anne Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1031	journal	November 2013
SAbDab: the structural antibody database Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1043	journal	November 2013
TheCandidaGenome Database: The new homology information page highlights protein similarity and phylogeny Binkley, Jonathan; Arnaud, Martha B.; Inglis, Diane O. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1046	journal	October 2013
MultitaskProtDB: a database of multitasking proteins Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1153	journal	November 2013
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
MMDB and VAST+: tracking structural similarities between macromolecular complexes Madej, Thomas; Lanczycki, Christopher J.; Zhang, Dachuan Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1208	journal	December 2013
SCOP2 prototype: a new approach to protein structure mining Andreeva, Antonina; Howorth, Dave; Chothia, Cyrus Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1242	journal	November 2013
PDBsum additions de Beer, Tjaart A. P.; Berka, Karel; Thornton, Janet M. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt940	journal	October 2013
STRING v10: protein–protein interaction networks, integrated over the tree of life Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1003	journal	October 2014
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease Shimoyama, Mary; De Pons, Jeff; Hayman, G. Thomas Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1026	journal	October 2014
The SUPERFAMILY 1.75 database in 2014: a doubling of data Oates, Matt E.; Stahlhacke, Jonathan; Vavoulis, Dimitrios V. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1041	journal	November 2014
IMGT®, the international ImMunoGeneTics information system® 25 years on Lefranc, Marie-Paule; Giudicelli, Véronique; Duroux, Patrice Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1056	journal	November 2014
ArrayExpress update—simplifying data submissions Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1057	journal	October 2014
Rfam 12.0: updates to the RNA families database Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1063	journal	November 2014
Genenames.org: the HGNC resources in 2015 Gray, Kristian A.; Yates, Bethan; Seal, Ruth L. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1071	journal	October 2014
COSMIC: exploring the world's knowledge of somatic mutations in human cancer Forbes, Simon A.; Beare, David; Gunasekaran, Prasad Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1075	journal	October 2014
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1117	journal	December 2014
Cancer3D: understanding cancer mutations through protein structures Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1140	journal	November 2014
The neXtProt knowledgebase on human proteins: current status Gaudet, Pascale; Michel, Pierre-André; Zahn-Zabal, Monique Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1178	journal	January 2015
CDD: NCBI's conserved domain database Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1221	journal	November 2014
The immune epitope database (IEDB) 3.0 Vita, Randi; Overton, James A.; Greenbaum, Jason A. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku938	journal	October 2014
CATH: comprehensive structural and functional annotations for genome sequences Sillitoe, Ian; Lewis, Tony E.; Cuff, Alison Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku947	journal	October 2014
SMART: recent updates, new developments and status in 2015 Letunic, Ivica; Doerks, Tobias; Bork, Peer Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku949	journal	October 2014
canSAR: an updated cancer research and drug discovery knowledgebase Tym, Joseph E.; Mitsopoulos, Costas; Coker, Elizabeth A. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1030	journal	December 2015
ChEBI in 2016: Improved services and an expanding collection of metabolites Hastings, Janna; Owen, Gareth; Dekker, Adriano Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1031	journal	October 2015
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1047	journal	October 2015
The Transporter Classification Database (TCDB): recent advances Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1103	journal	November 2015
DNA data bank of Japan (DDBJ) progress report Mashima, Jun; Kodama, Yuichi; Kosuge, Takehide Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1105	journal	November 2015
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors Rawlings, Neil D.; Barrett, Alan J.; Finn, Robert Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1118	journal	November 2015
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles Mathelier, Anthony; Fornes, Oriol; Arenillas, David J. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1176	journal	November 2015
GPCRdb: an information system for G protein-coupled receptors Isberg, Vignir; Mordalski, Stefan; Munk, Christian Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1178	journal	November 2015
Ensembl Genomes 2016: more genomes, more complexity Kersey, Paul Julian; Allen, James E.; Armean, Irina Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1209	journal	November 2015
Mouse genome database 2016 Bult, Carol J.; Eppig, Janan T.; Blake, Judith A. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1211	journal	November 2015
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1240	journal	November 2015
TheSaccharomycesGenome Database Variant Viewer Sheppard, Travis K.; Hitz, Benjamin C.; Engel, Stacia R. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1250	journal	November 2015
NONCODE 2016: an informative and valuable data source of long non-coding RNAs Zhao, Yi; Li, Hui; Fang, Shuangsang Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1252	journal	November 2015
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data Szklarczyk, Damian; Santos, Alberto; von Mering, Christian Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1277	journal	November 2015
ELM 2016—data update and new functionality of the eukaryotic linear motif resource Dinkel, Holger; Van Roey, Kim; Michael, Sushama Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1291	journal	November 2015
Biocuration of functional annotation at the European nucleotide archive Gibson, Richard; Alako, Blaise; Amid, Clara Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1311	journal	November 2015
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
The Reactome pathway Knowledgebase Fabregat, Antonio; Sidiropoulos, Konstantinos; Garapati, Phani Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1351	journal	December 2015
PubChem Substance and Compound databases Kim, Sunghwan; Thiessen, Paul A.; Bolton, Evan E. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv951	journal	September 2015
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
UniProt: the universal protein knowledgebase Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169 https://doi.org/10.1093/nar/gkw1099	journal	November 2016
The SWISS-MODEL Repository—new features and functionality Bienert, Stefan; Waterhouse, Andrew; de Beer, Tjaart A. P. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1132	journal	November 2016
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes Galperin, Michael Y.; Fernández-Suárez, Xosé M.; Rigden, Daniel J. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1188	journal	January 2017
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw962	journal	October 2016
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe Mir, Saqib; Alhroub, Younes; Anyango, Stephen Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1070	journal	November 2017
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection Rigden, Daniel J.; Fernández, Xosé M. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1235	journal	December 2017
The Protein Data Bank: a historical perspective Berman, Helen M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0108767307035623	journal	December 2007
Response toOn prompt update of literature references in the Protein Data Bank Berman, Helen M.; Burley, Stephen K.; Kleywegt, Gerard J. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10 https://doi.org/10.1107/S1399004714020513	journal	September 2014
Digital Design of Molecular Sculptures and Abstractions Meyer, Edgar F. Leonardo, Vol. 44, Issue 1 https://doi.org/10.1162/LEON_a_00089	journal	February 2011
Biomorphic Presentation of Proteins: Artistic Science or Scientific Art? Balaji, S. Leonardo, Vol. 46, Issue 3 https://doi.org/10.1162/LEON_a_00561	journal	June 2013
Protein Sculptures: Life's Building Blocks Inspire Art Voss-Andreae, Julian Leonardo, Vol. 38, Issue 1 https://doi.org/10.1162/leon.2005.38.1.41	journal	February 2005
Proteins, Immersive Games and Music Cai, Y. Y.; Lu, B. F.; Fan, Z. W. Leonardo, Vol. 39, Issue 2 https://doi.org/10.1162/leon.2006.39.2.135	journal	April 2006
Electronic Music for Bio-Molecules Using Short Music Phrases Shi, X. J.; Cai, Y. Y.; Chan, C. W. Leonardo, Vol. 40, Issue 2 https://doi.org/10.1162/leon.2007.40.2.137	journal	April 2007
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources Bousfield, David; McEntyre, Johanna; Velankar, Sameer F1000Research, Vol. 5 https://doi.org/10.12688/f1000research.7911.1	journal	February 2016
Bioinformatics and Management Science: Some Common Tools and Techniques Abbas, Ali E.; Holmes, Susan P. Operations Research, Vol. 52, Issue 2 https://doi.org/10.1287/opre.1030.0095	journal	April 2004
Citing a Data Repository: A Case Study of the Protein Data Bank Huang, Yi-Hung; Rose, Peter W.; Hsu, Chun-Nan PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0136631	journal	August 2015
Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank" Basner, Jodi RCSB Protein Data Bank https://doi.org/10.2210/rcsb_pdb/pdb-cit-anal-2017	journal	May 2017
Analysis of Impact Metrics for the Protein Data Bank Markosian, Christopher; Costanzo, Luigi Di; Sekharan, Monica Figshare https://doi.org/10.6084/m9.figshare.c.4064561	collection	January 2018

Cited By (2)

DRAMP 2.0, an updated data repository of antimicrobial peptides Kang, Xinyue; Dong, Fanyi; Shi, Cheng Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0154-y	journal	August 2019
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1004	journal	October 2018

Linked Research (9)

Similar Records

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

Journal Article · 2025 · Quarterly Reviews of Biophysics · OSTI ID:3018428

Berman, Helen M.; Burley, Stephen K.

rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

Journal Article · 2025 · Journal of Molecular Biology · OSTI ID:2515681

Piehl, Dennis W.; Vallat, Brinda; Truong, Ivana; +13 more

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Journal Article · 2021 · Protein Science · OSTI ID:1997062

Zardecki, Christine; Dutta, Shuchismita; Goodsell, David S.; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
databases
literature mining
publishing
science and technology
structural biology

Data Set: Web of Science Data Costanzo, Luigi Di; Shao, Chenghua https://doi.org/10.6084/m9.figshare.6121322 The current record is supplemented by this dataset	dataset	January 2018
Data Set: Web of Science Data Costanzo, Luigi Di; Shao, Chenghua https://doi.org/10.6084/m9.figshare.6121322.v1 The current record is supplemented by this dataset	dataset	January 2018
2017 RCSB.org Survey Data Zardecki, Christine; Markosian, Christopher https://doi.org/10.6084/m9.figshare.6121394 The current record is supplemented by this dataset	dataset	January 2018
2017 RCSB.org Survey Data Zardecki, Christine; Markosian, Christopher https://doi.org/10.6084/m9.figshare.6121394.v1 The current record is supplemented by this dataset	dataset	January 2018
Network Visualization Map Data Costanzo, Luigi Di; Markosian, Christopher https://doi.org/10.6084/m9.figshare.6121436 The current record is supplemented by this dataset	dataset	January 2018
Network Visualization Map Data Costanzo, Luigi Di; Markosian, Christopher https://doi.org/10.6084/m9.figshare.6121436.v1 The current record is supplemented by this dataset	dataset	January 2018
NAR Molecular Biology Database Collection Data Zardecki, Christine; Sekharan, Monica; Shao, Chenghua https://doi.org/10.6084/m9.figshare.6122099 The current record is supplemented by this dataset	dataset	January 2018
NAR Molecular Biology Database Collection Data Zardecki, Christine; Sekharan, Monica; Shao, Chenghua https://doi.org/10.6084/m9.figshare.6122099.v1 The current record is supplemented by this dataset	dataset	January 2018
Analysis of Impact Metrics for the Protein Data Bank Markosian, Christopher; Costanzo, Luigi Di; Sekharan, Monica https://doi.org/10.6084/m9.figshare.c.4064561 The current record is supplemented by this collection	collection	January 2018