Engineering Commons^™

Multisequence Algorithm For Coarse-Grained Biomolecular Simulations: Exploring The Sequence-Structure Relationship Of Proteins, Adekunle Aina, Stefan Wallin

Association in Solution IV

Many biologically motivated problems naturally call for the investigation and comparison of molecular variants, such as determining the mechanisms of specificity in biomolecular interactions or the mechanisms of molecular evolution. We consider a generalized ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are shallower or absent. We test the method on an intermediate-resolution coarse-grained …