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» Protein Folding Simulation in CCP
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CODES
2005
IEEE
14 years 1 months ago
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
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...
BMCBI
2004
123views more  BMCBI 2004»
13 years 7 months ago
Interaction profile-based protein classification of death domain
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...
Drew Lett, Michael Hsing, Frederic Pio
BMCBI
2010
141views more  BMCBI 2010»
13 years 8 months ago
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models
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...
Franziska Hoffgaard, Philipp Weil, Kay Hamacher
GRID
2007
Springer
14 years 2 months ago
Grid-based asynchronous replica exchange
— 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...
Zhen Li, Manish Parashar
IPPS
2006
IEEE
14 years 1 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
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...