Struct-NB: predicting protein-RNA binding sites using structural features
International Journal of Data Mining and Bioinformatics
Computational Biology and Chemistry
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We analyzed the structural properties and the local sur- face environment of surface amino acid residues of pro- teins using a large, non-redundant dataset of 2383 pro- tein chains in dimeric complexes from PDB. We compared the interface residues and non-interface residues based on six properties: side chain orientation, surface roughness, solid angle, cx value, hydrophobicity and interface cluster size. The results of our analysis show that interface residues have side chains pointing inward; interfaces are rougher, tend to be flat, moderately convex or concave and protrude more relative to non-interface surface residues. Interface residues tend to be surrounded by hydrophobic neighbors and tend to form clusters consisting of three or more in- terfaces residues. These findings are consistent with pre- vious published studies using much smaller datasets, while allowing for more qualitative conclusions due to our larger dataset. Preliminary results suggest the possibility of using the six the properties to identify putative interface residues.