This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of pro...
Robert S. Germain, Blake G. Fitch, Aleksandr Raysh...
Background: The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experim...
Background: One of the most challenging aspects of biomolecular systems is the understanding of the coevolution in and among the molecule(s). A complete, theoretical picture of th...
— Replica exchange is a powerful sampling algorithm and can be effectively used for applications such as simulating the structure, function, folding, and dynamics of proteins and...
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...