Biased Monte Carlo optimization of protein sequences

Abstract

The biased Monte Carlo method is used to optimize the amino acid sequences. The sequences optimized from the approach are then compared with conventional Monte Carlo and a self-consistent mean-field (SCMF) method. For more complex systems, the biased Monte Carlo method is found to be more efficient. However, biased Monte Carlo does not converge as quickly as SCMF, but often found better sequences.