Characterizing and predicting catalytic residues in enzyme active sites based on local properties: a machine learning approach
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Patarroyo, Manuel A.
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Developing computational methods for assigning protein function from tertiary structure is a very important problem, predicting a catalytic mechanism based only on structural information being a particularly challenging task. This work focuses on helping to understand the molecular basis of catalysis by exploring the nature of catalytic residues, their environment and characteristic properties in a large data set of enzyme structures and using this information to predict enzyme structures' active sites. A machine learning approach that performs feature extraction, clustering and classification on a protein structure data set is proposed. The 6,376 residues directly involved in enzyme catalysis, present in more than 800 proteins structures in the PDB were analyzed. Feature extraction provided a description of critical features for each catalytic residue, which were consistent with prior knowledge about them. Results from k-fold-cross-validation for classification showed more than 80% accuracy. Complete enzymes were scanned using these classifiers to locate catalytic residues.
Biochemistry , Machine learning , Sequences , Genomics , Bioinformatics , Predictive models , Protein engineering , Nuclear magnetic resonance , Data mining , Crystallography