FROST: revisited and distributed

FROST (Fold Recognition-Oriented Search Tool) [A. Marin et al., (2002)] is a software whose purpose is to assign a 3D structure to a protein sequence. It is based, on a series of filters and uses a database of about 1200 known 3D structures, each one associated, with empirically determined score distributions. FROST uses these distributions to normalize the score obtained, when a protein sequence is aligned, with a particular 3D structure. Computing these distributions is extremely time consuming; it requires solving about 1,200,000 hard combinatorial optimization problems and takes about 40 days on a 2.4 GHz computer. This paper describes how FROST has been successfully redesigned and structured, in modules and independent tasks. The new package organization allows these tasks to be distributed and executed, in parallel using a centralized, dynamic load balancing strategy. On a cluster of 12 PCs, computing the score distributions takes now about 3 days, which represents a parallelization efficiency of about 1.