Protein surface characterization using an invariant descriptor

Aim. To develop a new invariant descriptor for the characterization of protein surfaces, suitable for various analysis tasks, such as protein functional classification, and search and retrieval of protein surfaces over a large database. Methods. We start with a local descriptor of selected circular patches on the protein surface. The descriptor records the distance distribution between the central residue and the residues within the patch, keeping track of the number of particular pairwise residue cooccurrences in the patch. A global descriptor for the entire protein surface is then constructed by combining information from the local descriptors. Our method is novel in its focus on residue-specific distance distributions, and the use of residue-distance co-occurrences as the basis for the proposed protein surface descriptors. Results. Results are presented for protein classification and for retrieval for three protein families. For the three families, we obtained an area under the curve for precision and recall ranging from 0.6494 (without residue co-occurrences) to 0.6683 (with residue co-occurrences). Large-scale screening using two other protein families placed related family members at the top of the rank, with a number of uncharacterized proteins also retrieved. Comparative results with other proposed methods are included.