Rapid Catalytic Template Searching as an Enzyme Function Prediction ProcedureReportar como inadecuado

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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.

Autor: Jerome P. Nilmeier, Daniel A. Kirshner, Sergio E. Wong, Felice C. Lightstone

Fuente: http://plos.srce.hr/


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