A divide and conquer approach to fast loop modeling

Abstract

We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 Å RMSD for three-residue loops and 3.72 Å RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations.