Journal of Chemical Physics, Vol.109, No.7, 2895-2903, 1998
Exploring the space of protein folding Hamiltonians : The balance of forces in a minimalist beta-barrel model
A rapid and effective method for obtaining thermodynamic quantities for Hamiltonians whose configurational space has not been examined through a direct simulation has been developed. This approach extends the scope of the weighted histogram analysis method and is applied to the exploration of the balance of forces within the off-lattice Honeycutt-Thirumalai 46-mer beta-barrel model. Specificity is introduced into the long range hydrophobic interactions by scaling back the non-native attractive component of the hydrophobic interactions through a scaling factor lambda (0
Keywords:MONTE-CARLO SIMULATION;NUCLEATION MECHANISM;GLOBULAR-PROTEINS;FOLDED STATES;TRANSITION;SEQUENCES;PATHWAYS;KINETICS