Free energy calculations for peptides via deterministic global optimization

摘要: The αBB algorithm is a deterministically based global optimization method that has been successfully used to locate the minimum energy conformations of peptide systems. goal this procedure identify native conformation given by identifying structure possessing potential energy. However, rigorous conformational search should exhibiting free In work, novel methods are developed for locating and clusters peptides. These on an harmonic approximation entropic effects, which requires ability generate dense ensemble distinct low local minima. Two approaches, both general concepts branch bound framework, these ensembles. performing calculations, potential-energy contributions were modeled using all-atom force field. addition, hydration effects also considered utilizing solvent-accessible volume shell model. analysis was applied unsolvated solvated forms met- leu-enkephalin. It found produce dense, Boltzmann-type, distributions low-energy metastable states. inclusion influence prediction statistical treatment thermodynamics folding showed transition temperature, signified collapse from high energy, extended structures ground-statelike ensemble, could be identified.