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Cellobiohydrolase
Xiaohu Hu
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Scaling of Multimillion-Atom MD Simulation on Petascale Supercomputers
Petascale MD: Scaling of Multimillion-Atom MD Simulation on Petascale Supercomputers
Performance RF
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer: A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The ...
Jaguar Supercomputer: http://www.flickr.com/photos/oakridgelab/3592579288/
2006
2008
in press
Nucleotide-Dependence of G-Actin Conformation from Multiple Molecular Dynamics Simulations and Observation of a Putatively Polymerization-Competent Superclosed State.: The assembly of monomeric G-actin into filamentous F-actin is nucleotide dependent: ATP-G-actin is favored for filament growth at the barbed end of F-actin, ...
A Molecular Mechanics Force Field for Lignin: A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial ...
The QM/MM Molecular Dynamics and Free Energy Simulations of the Acylation Reaction Catalyzed by the Serine-Carboxyl Peptidase Kumamolisin-As.: Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations are performed to study the acylation reaction catalyzed by ...
REACH: A Program for Coarse-Grained Biomolecular Simulation: REACH ( R ealistic E xtension A lgorithm via C ovariance H essian) is a program package for residue-scale coarse-grained biomolecular simulation. The program ...
A Peptide-Linkage Deletion Procedure for Estimate of Energetic Contributions of Individual Peptide Groups in a Complex Environment: Application to Parallel β-Sheets: A peptide-linkage deletion procedure is introduced for extracting the quantum merchanical (QM) interaction energies of individual groups in a complex ...
Molecular-Dynamics Simulations of ELIC - a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor.: The ligand-gated ion channel from Erwinia chrysanthemi (ELIC) is a prokaryotic homolog of the eukaryotic nicotinic acetylcholine receptor (nAChR) that responds ...
QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates.
Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes.
An Improved Poisson-Boltzmann Solver Using an Adaptive Fast Multipole Method.
Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase.: Glutamate racemases (EC 5.1.1.3) catalyze the cofactor-independent stereoinversion of d- and l-glutamate and are important for viability in several ...
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding: Changes in the free energy barrier (DeltaE), entropy, and motional parameters associated with the rotation of methyl groups in a protein (calmodulin (CaM)) on ...
Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping.: The proton pumping cycle of bacteriorhodopsin consists of five consecutive proton transfer steps, in all of which water molecules are likely to play critical ...
Coarse-Grained Force Field for the Nucleosome from Self-Consistent Multiscaling: A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA ...
Partitioning of Amino-Acid Analogues in a Five-Slab Membrane Model.: The positional preferences of the twenty amino-acid residues in a phospholipid bilayer are investigated by calculating the solvation free energy of the ...
Cellulosic Ethanol: Progress towards a Simulation Model of Lignocellulosic Biomass: A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial ...
Dual Function of the Hydration Layer around an Antifreeze Protein Revealed by Atomistic Molecular Dynamics Simulations: Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura ...
Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation: Abstract: A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding ...
Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space.: Molecular dynamics simulation of oligopeptide chains reveals configurational subdiffusion at equilibrium extending from 10(-12) to 10(-8) s. Trap models, ...

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Search results — 150 items matching your search terms