A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins.
The problem of global optimization is pivotal in a variety of scientific fields. Here, we present a robust stochastic search method that is able to find the global minimum for a given cost function, as well as, in most cases, any number of best solutions for very large combinatorial "explosive" systems. The algorithm iteratively eliminates variable values that contribute consistently to the highest end of a cost function's spectrum of values for the full system. Values that have not been eliminated are retained for a full, exhaustive search, allowing the creation of an ordered population of best solutions, which includes the global minimum. We demonstrate the ability of the algorithm to explore the conformational space of side chains in eight proteins, with 54 to 263 residues, to reproduce a population of their low energy conformations. The 1,000 lowest energy solutions are identical in the stochastic (with two different seed numbers) and full, exhaustive searches for six of eight proteins. The others retain the lowest 141 and 213 (of 1,000) conformations, depending on the seed number, and the maximal difference between stochastic and exhaustive is only about 0.15 Kcal/mol. The energy gap between the lowest and highest of the 1,000 low-energy conformers in eight proteins is between 0.55 and 3.64 Kcal/mol. This algorithm offers real opportunities for solving problems of high complexity in structural biology and in other fields of science and technology.
Glick
Meir
M
Department of Medicinal Chemistry and the David R. Bloom Center for Pharmacy, School of Pharmacy, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
Rayan
Anwar
A
Goldblum
Amiram
A
D000465:Algorithms; D055592:Biophysical Phenomena; D001703:Biophysics; D019151:Peptide Library; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013269:Stochastic Processes; D013816:Thermodynamics
D019151:Peptide Library; D011506:Proteins