Database Resources of the National Center for Biotechnology Information
Open accessAbstract
nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include iCn3D, MutaBind, and the Antimicrobial Resistance Gene Reference Database; and resources that were updated in the past year include My Bibliography, SciENcv, the Pathogen Detection Project, Assembly, Genome, the Genome Data Viewer, BLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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Tools such as DIGIT and Abysis source their data from the European Nucleotide Archive (ENA) and the National Center for Biotechnology Information (NCBI); their sequence volumes are of the order of 105 and contain multiple artificially engineered sequences.
“Tools such as DIGIT and Abysis source their data from the European Nucleotide Archive (ENA) [60] and the National Center for Biotechnology Information (NCBI) [61]; their sequence volumes are of the order of 105 and contain multiple artificially engineered sequences.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [61]
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Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
PubChem Substance and Compound databases
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436 · see citing works
Clark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1276 · Cited by 1,471 · see citing works
Database resources of the National Center for Biotechnology Information
Coordinators, N. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1290 · Cited by 1,459 · see citing works
Self-citationSchäffer, A. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.14.2994 · Cited by 1,375 · see citing works
IgBLAST: an immunoglobulin variable domain sequence analysis tool
Ye, J., Ma, N., Madden, T., & Ostell, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt382 · Cited by 1,161 · see citing works
COBALT: constraint-based alignment tool for multiple protein sequences
Papadopoulos, J. S., & Agarwala, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm076 · Cited by 1,130 · see citing works
[10] Entrez: Molecular biology database and retrieval system
Schuler, G. D., Epstein, J. A., Ohkawa, H., & Kans, J. A. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66012-1 · Cited by 435 · see citing works
Assembly: a resource for assembled genomes at NCBI
Kitts, P. A., Church, D. M., Thibaud-Nissen, F., Choi, J., Hem, V., Sapojnikov, V., Smith, R. G., Tatusova, T., Xiang, C., Zherikov, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1226 · Cited by 398 · see citing works
Cn3D: sequence and structure views for Entrez
Wang, Y., Geer, L. Y., Chappey, C., Kans, J. A., & Bryant, S. H. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01561-9 · Cited by 274 · see citing works
Draizen, E. J., Shaytan, A. К., Mariño‐Ramírez, L., Talbert, P. B., Landsman, D., & Panchenko, A. R. (2016) · Database · doi:10.1093/database/baw014 · Cited by 152 · see citing works
MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions
Li, M., Simonetti, F. L., Goncearenco, A., & Panchenko, A. R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw374 · Cited by 118 · see citing works
Flagged first, then by citations
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Sorted by citations
Day, F., Karaderi, T., Jones, M. R., Meun, C., He, C., Drong, A., Kraft, P., Lin, N., Huang, H., Broer, L., et al. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007813 · Cited by 619 · see citing works
Kovaltsuk, A., Leem, J., Kelm, S., Snowden, J., Deane, C. M., & Krawczyk, K. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800708 · Cited by 247 · see citing works
Ciallella, H. L., & Zhu, H. (2019) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.8b00393 · Cited by 227 · see citing works
Computational approaches to therapeutic antibody design: established methods and emerging trends
Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbz095 · Cited by 219 · see citing works
The BRENDA enzyme information system–From a database to an expert system
Schomburg, I., Jeske, L., Ulbrich, M., Placzek, S., Chang, A., & Schomburg, D. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.04.020 · Cited by 222 · see citing works
Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials
Choudhary, A., Naughton, L., Montánchez, I., Dobson, A., & Rai, D. (2017) · Marine Drugs · doi:10.3390/md15090272 · Cited by 138 · see citing works
A structure-informed atlas of human-virus interactions
Lasso, G., Mayer, S. V., Winkelmann, E. R., Chu, T., Elliot, O., Patino-Galindo, J. A., Park, K., Rabadan, R., Honig, B., & Shapira, S. D. (2019) · Cell · doi:10.1016/j.cell.2019.08.005 · Cited by 133 · see citing works
Reimschuessel, R., Grabenstein, M., Guag, J., Nemser, S. M., Song, K., Qiu, J., Clothier, K. A., Byrne, B. A., Marks, S. L., Cadmus, K., et al. (2017) · Journal of Clinical Microbiology · doi:10.1128/jcm.02137-16 · Cited by 105 · see citing works
Brief Report: A Survey of Autism Research Priorities Across a Diverse Community of Stakeholders
Frazier, T. W., Dawson, G., Murray, D., Shih, A., Sachs, J. S., & Geiger, A. (2018) · Journal of Autism and Developmental Disorders · doi:10.1007/s10803-018-3642-6 · Cited by 97 · see citing works
sdAb-DB: the single domain antibody database
Wilton, E. E., Opyr, M. P., Kailasam, S., Kothe, R. F., & Wieden, H.-J. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00407 · Cited by 84 · see citing works
Mudge, J. M., Jungreis, I., Hunt, T., Gonzalez, J. M., Wright, J. C., Kay, M., Davidson, C., Fitzgerald, S., Seal, R., Tweedie, S., et al. (2019) · Genome Research · doi:10.1101/gr.246462.118 · Cited by 80 · see citing works
Thalia: semantic search engine for biomedical abstracts
Soto, A. J., Przybyła, P., & Ananiadou, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty871 · Cited by 60 · see citing works
Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.09.031 · Cited by 62 · see citing works
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1
Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., et al. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00752 · Cited by 28 · see citing works
Peter, H. L., Giglberger, M., Frank, J., Streit, F., Zänkert, S., Kreuzpointner, L., Rietschel, M., Kudielka, B. M., & Wüst, S. (2022) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2022.105883 · Cited by 4 · see citing works
- Authors
- Coordinators, N. R.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- NCBI Resource Coordinators
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-28
- Volume
- 45
- Issue
- D1
- Pages
- D12-D17
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5210554
- OpenAlex
- W4234797890
- Cited by
- 817
- References
- 12
- Citations by year
- 2026: 6 · 2025: 23 · 2024: 26 · 2023: 25 · 2022: 65 · 2021: 69 · 2020: 104 · 2019: 147 · 2018: 220 · 2017: 126 · 2016: 3 · 2015: 1
- FWCI
- 85.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- Entrez, BLAST, PubMed, antimicrobial resistance genes, genomic databases, SciENcv, PubChem
- MeSH terms
- Drug Resistance, Microbial, National Library of Medicine (U.S.), United States, Sequence Alignment, Genome, Bacterial, Systems Integration, Genomics, Databases, Genetic, Databases, Protein, PubMed, Databases, Chemical
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