ArticleNucleic acids research2013
Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm.Journal of cheminformatics · 2024Article
- pyScoMotif: discovery of similar 3D structural motifs across proteins.Bioinformatics advances · 2023Article
- Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Evaluation of model refinement in CASP14.Proteins · 2021Article
- Real-time structural motif searching in proteins using an inverted index strategy.PLoS computational biology · 2020Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris.BMC bioinformatics · 2019Article
- A Monoclonal Antibody to Cryptococcus neoformans Glucuronoxylomannan Manifests Hydrolytic Activity for Both Peptides and Polysaccharides.The Journal of biological chemistry · 2017Article
- Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.Advances in experimental medicine and biology · 2016Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- An assessment of catalytic residue 3D ensembles for the prediction of enzyme function.BMC bioinformatics · 2015Article
- Basis for substrate recognition and distinction by matrix metalloproteinases.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
3 authors.
Funding
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Abstract
The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.
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