ArticlePloS one2013
Rapid catalytic template searching as an enzyme function prediction procedure.
Article in PloS one, 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.
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.Journal of molecular biology · 2022Article
- System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris.BMC bioinformatics · 2019Article
- CSmetaPred: a consensus method for prediction of catalytic residues.BMC bioinformatics · 2017Article
- GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.Nucleic acids research · 2017Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
- A Monoclonal Antibody to Cryptococcus neoformans Glucuronoxylomannan Manifests Hydrolytic Activity for Both Peptides and Polysaccharides.The Journal of biological chemistry · 2017Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.Advances in experimental medicine and biology · 2016Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.Trends in biochemical sciences · 2014Review
- A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations.PloS one · 2014Article
- Article
- Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.Nucleic acids research · 2013Article
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4 authors.
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Abstract
We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues--The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches.
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