Large Scale Protein Side-chain Packing Based on Maximum Edge-weight Clique Finding Algorithm

The protein side-chain packing problem (SCPP) is known to be NP-complete. Various graph theoretic based side-chain packing algorithms have been proposed. However as the size of the protein becomes larger, the sampling space increases exponentially. Hence, one approach to cope with the time complexity is to decompose the graph of the protein into smaller subgraphs. Some existing approaches decompose the graph into biconnected components at an articulation point (resulting in an at-most 21-residue subgraph) or solve the SCPP by tree decomposition (4-, 5-residue subgraph). In this regard, we had also presented a deterministic based approach called as SPWCQ using the notion of maximum edge weight clique in which we reduce SCPP to a graph and then obtain the maximum edge-weight clique of the obtained graph. This algorithm performs well for a protein of less than 500 residues. However, it fails to produce a feasible solution for larger proteins because of the size of the search space. In this paper, we present a new heuristic approach for the side-chain packing problem based on the maximum edge-weight clique finding algorithm that enables us to compute the side-chain packing of much larger proteins. Our new approach can compute side-chain packing of a protein of 874 residues with an RMSD of 1.423${\AA}$.