The inverse protein folding problem on 2D and 3D lattices

In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model on 3D and 2D lattices [13, 26]. In this problem, we are given a contact graph G = (V,E) of a protein sequence that is embeddable in a 3D (respectively, 2D) lattice and an integer 1 ≤ K ≤ |V |. The goal is to find an induced subgraph of G of at most K vertices with the maximum number of edges. In this paper, we prove the following results: A preliminary version of this paper without many proofs appeared in 15th Annual Combinatorial Pattern Matching Symposium, LNCS 3109, C. S. Sahinalp, S. Muthukrishnan and U. Dogrusoz (editors), pp. 244-253, July 2004. Supported by NSF grant CCR-O208821. Supported by NSF grants CCR-0296041, CCR-0206795 and CCR-0208749. Supported by NSF grant DMS-9970325. Supported in part by NSF grant CCR-0208749.