Paper Citing NAMD - Abstract
Balaji, N.; Ramya, L.; Gautham, N.
THE INHERENT STRUCTURE LANDSCAPE OF MET-ENKEPHALIN DETERMINED BY THE MOLS TECHNIQUE
BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE RAMACHANDRAN MAP, 492-502, 2013
We have developed a method, called the MOLS method (for mutually orthogonal Latin squares) to exhaustively explore the conformational space of small peptides. Here we used this method to delineate the inherent structure (IS) landscape of the pentapeptide Met-Enkephalin at and above 'room temperature'. Inherent structures have been defined as structures located at the minima of the energy landscape. From the IS landscape we extracted the probability density and calculated the density of states. To compare the results, we have also sampled the conformations for the peptide through molecular dynamics simulations and periodic rapid quenching. The probability density distributions followed a similar pattern in both methods.
