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A FAST AND EFFECTIVE CONFORMATIONAL SEARCH METHOD FOR PEPTIDES
Preview AbstractWe propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.
SIMULATIONS OF PEPTIDE MODELS IN A SOLVENT
Preview AbstractThe three-dimensional structures of the heptapeptide deltorphin (H-Tyr1-D-Met2-Phe3-His4-Leu5-Met6-Asp7-NH2) are studied in aqueous solution using Energy Landscape Paving (ELP) method. The effect of a solvation energy term on the conformations are determined by analyzing Ramachandran plots. The structures are compared with experimental NMR data. By minimizing the energy structures, the low-energy microstates of the molecule in aqueous solution are determined.
A COMBINATION OF REPLICA EXCHANGE MONTE CARLO AND ENERGY LANDSCAPE PAVING ALGORITHMS TO INCREASE THE EFFECTIVENESS OF CONFORMATIONAL SAMPLING
Preview AbstractA combination of replica exchange Monte Carlo sampling techniques and energy landscape paving approach is presented. This hybrid algorithm combines the features of the energy landscape paving (ELP) and replica exchange methods (REM). I have tested its performance in studying the low-energy conformations of the benchmark peptide Met-enkephalin.