A kinase sequence database: sequence alignments and family assignment
Abstract
Summary: The Kinase Sequence Database (KSD) located at http://kinase.ucsf.edu/ksd contains information on 290 protein kinase families derived by profile-based clustering of the non-redundant list of sequences obtained from a GenBank-wide search. Included in the database are a total of 5041 protein kinases from over 100 organisms. Clustering into families is based on the extent of homology within the kinase catalytic domain (250–300 residues in length). Alignments of the families are viewed by interactive Excel-based sequence spreadsheets. In addition, KSD features evolutionary trees derived for each family and detailed information on each sequence as well as links to the corresponding GenBank entries. Sequence manipulation tools, such as evolutionary tree generation, novel sequence assignment, and statistical analysis, are also provided. Availability: The kinase sequence database is a web-based service accessible at http://kinase.ucsf.edu/ksd Contact: buzko@cmp.ucsf.edushokat@cmp.ucsf.edu/ksd * To whom correspondence should be addressed.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Allosteric sites are diverse and confer better selectivity among homologous proteins, resulting in fewer side effects and greater value in clinical applications.
“Secondly, allosteric sites are diverse and confer better selectivity among homologous proteins, resulting in fewer side effects and greater value in clinical applications.”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [244]
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515 · see citing works
[22] Using CLUSTAL for multiple sequence alignments
Higgins, D. G., Thompson, J., & Gibson, T. J. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66024-8 · Cited by 1,571 · see citing works
Hanks, S. K., & Quinn, A. M. (1991) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(91)00126-h · Cited by 1,232 · see citing works
Generation of Monospecific Nanomolar Tyrosine Kinase Inhibitors via a Chemical Genetic Approach
Bishop, A. C., Kung, C.-Y., Shah, K., Witucki, L. A., Shokat, K. M., & Liu, Y. (1999) · Journal of the American Chemical Society · doi:10.1021/ja983267v · Cited by 154 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials
Xie, X., Yu, T., Li, X., Zhang, N., Foster, L. J., Peng, C., Huang, W., & He, G. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01589-z · Cited by 396 · see citing works
Covalent Inhibition in Drug Discovery
Ghosh, A. K., Samanta, I., Mondal, A., & Liu, W. R. (2019) · ChemMedChem · doi:10.1002/cmdc.201900107 · Cited by 265 · see citing works
- Authors
- Buzko, O., & Shokat, K. M.
- Affiliations
- University of California, San Francisco (US)
- ORCID
- Shokat, Kevan M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-09-01
- Volume
- 18
- Issue
- 9
- Pages
- 1274-1275
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2134399756
- Cited by
- 58
- References
- 5
- Citations by year
- 2023: 2 · 2021: 3 · 2020: 2 · 2019: 5 · 2018: 1 · 2017: 1 · 2016: 6 · 2015: 2 · 2014: 5 · 2013: 3 · 2012: 2
- FWCI
- 1.04
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Keywords
- protein kinases, protein kinase families, sequence clustering, sequence alignment, catalytic domain, phylogenetic tree, sequence homology, online databases
- MeSH terms
- Database Management Systems, Protein Kinases, Cluster Analysis, Information Storage and Retrieval, Sequence Alignment, Sequence Homology, Internet, Sequence Analysis, Protein, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
