Publications
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Case, D.A.,
Walker, R.C. et al.
AMBER
11, 2010, University of
California, San Francisco. |
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Goetz, A.W., Woelfe,
T., Walker, R.C., "Quantum Chemistry on Graphics
Processing Units", Ann. Rev. Comp. Chem., 2010,
Accepted. |
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Xu, D., Williamson,
M.J., Walker, R.C., "Advancements in Molecular Dynamics
Simulations of Biomolecules on Graphical Processing
Units.", Ann. Rev. Comp. Chem., 2010, Accepted |
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Lawrenz, M., Wereszczynski, J., Amaro,
R., Walker, R.C., Roitberg, A.E., McCammon, J.A.,
"Impact of calcium on N1 influenza neuraminidase
dynamics and binding free energy", Proteins, 2010,
in press. |
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Zhong, L., Walker, R.C., Brady, J.W. et al.,
"Computational Simulations of the Trichoderma reesei
Cellobiohydrolase I Acting on Microcrystalline Cellulose
Iβ: The Enzyme-Substrate Complex", Carb. Res., 2009,
344, 1984-1992. (Full
Text PDF) |
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Seabra, G.M., Walker, R.C., Roitberg, A.E.,
"Are Current
Semi-Empirical Methods Better than Force Fields? A Study
from the Thermodynamics Perspective", J. Phys. Chem. A.,
2009, 113, 11938-11948. (Full
Text PDF) |
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Bergonzo, C., Campbell, A.J., Walker, R.C., Simmerling,
C., "A Partial Nudged Elastic Band Implementation for
Use with Large or Explicitly Solvated Large Systems",
Int. J. Quant. Chem., 2009, 109, 15, 3781-3790. (Full
Text PDF) |
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Crowley, M.F., Williamson, M.J., Walker, R.C.,
"CHAMBER:
Comprehensive Support for CHARMM Force Fields Within the
AMBER Software", Int. J. Quant. Chem., 2009, 109, 15,
3767-3772. (Full
Text PDF) |
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Sherrill C.D., Sumpter B.G.,
Sinnokrot M.O., Marshall M.S., Hohenstein E.G.,
Walker R.C., Gould I.R., "Assessment of standard
force field models against high-quality ab initio
potential curves for prototypes of -, CH/, and SH/
interactions", J. Comp. Chem, 2009, 30, 2187-2193. (Full
Text PDF) |
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Crowley, M. F.; Uberbacher, E. C.; Brooks, C. L., III;
Walker, R. C.; Nimlos, M. R.; Himmel, M. E., "Developing
improved MD codes for understanding processive
cellulases", SCIDAC 2008: Scientific Discovery Through
Advanced Computing, 2008, 125: 12049-12049. (Full
Text PDF) |
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Sharikov, Y.,
Walker, R.C., Greenberg, J., Kouznetsova, V., Nigam, S.,
Miller, M.A., Masliah, E., Tsigelny, I.F., "MAPAS: a
tool for prediction of membrane-contacting protein
surfaces" Nature: Methods, 2008, 5(2), 119. (Full
Text PDF,
Supplemental Material PDF) |
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Case, D.A.,
Walker, R.C. et al.
AMBER
10, 2008, University of
California, San Francisco. |
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Walker, R.C., Crowley, M.F., Case, D.A., "The
Implementation of a Fast and Accurate QM/MM Potential
Method in AMBER." J. Comp. Chem. 2008, 29,
1019-1031. (Full
Text PDF,
Supplemental Material PDF) |
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Seabra, G.M.,
Torras-Costa, J., Walker, R.C., Roitberg, A.E. "Mixed
QM/MM calculations in Biological Systems" John von
Neumann Institut fur Computing, NIC Series, 2007,
34, 37-43 (Full
Text PDF) |
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Zhong, L.
Walker, R.C, Brady, J.W. et al. "Interactions of
the Complete Cellobiohydrolase I from Trichodera reesei
with Microcrystalline Cellulose IB.", Cellulose.
2008, 15, 261-273 (Full
Text PDF) |
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Raman, S., Bin,
Q., Baker, D., Walker, R.C. "Advances in Protein
Structure Prediction on Massively Parallel Systems:
Recent Successes with the Rosetta Software and Future
Directions.", IBM Journal of R and D. 2008,
5, 7-17 (Full
Text PDF) |
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Seabra, G.M,
Walker, R.C., Elstner, M., Case, D.A., Roitberg, A.E.,
"Implementation of the SCC-DFTB Method for Hybrid QM/MM
Simulations within the Amber Molecular Dynamics
Package.", J. Phys. Chem A. 2007, 111,
5655-5664. (Full
Text PDF) |
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Nimlos, M.R.,
Walker, R.C. Himmel, M. et al., "Molecular
Modeling Suggests Induced Fit of Family I Carbohydrate
Binding Modules with a Broken Chain Cellulose Surface.",
Prot. Eng., Des and Sel. 2007, 20(4),
179-187. (Full
Text PDF) |
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Walker, R.C.,
Gould, I.R., Klug, D.R. "A Comparison of the Performance
of Ab Initio, DFT and Semi- Empirical Methods for
Probing Equilibrium Fluctuations." J. Comp. Chem.,
2007, 28(2), 478-490
(Full
Text PDF) |
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Case, D.A.,
Walker, R.C. et al.
AMBER
9, (2006),
University of California, San
Francisco. |
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Walker, R.C.,
Cho, B.M., Amer, H., Mercer, I.P., Gould, I.R., Klug,
D.R., "The effect of adiabaticity on electron dynamics
in Zinc Myoglobin." J. Phys. Chem. B., 2005,
109(12), 5954-5961. (Full
Text PDF) |
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Case, D.A., Crowley,
M.F., Walker, R.C. et al. "Computer Modeling of
Proteins and Nucleic Acids", Sci. Rep. of The Scripps
Research Institute. 2005, 189-190. |
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Case, D.A., Crowley,
M.F., Walker, R.C. et al. "Computer Modeling of
Proteins and Nucleic Acids", Sci. Rep. of The Scripps
Research Institute. 2004, 182-184. |
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Walker, R.C.,
Klug, D.R. et al. "Large and fast relaxations inside a
protein: Calculation and measurement of reorganisation
energies in alcohol dehydrogenase.", J. Phys. Chem.
B., 2002, 106(46). 11658-11665
(Full
Text PDF) |
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Collected Works
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Tsigelny, I.F.,
Sharikov, Y., Walker, R.C., Greenberg, J., Kouznetsova,
V., Miller, M.A., Masliah, E., "Membrane-active
peptides: methods and results on structure and
function", Ed. M. Castanha, International University
Line, La Jolla, CA, 2010,
ISBN: 978-0-9720774-5-3 |
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Chapter
entitled "Computer Simulations of Cellulase", in
"Biomass Recalcitrance", Ed. Dr. M. Himmel, NREL,
Blackwell Publishing, Oxford, UK, 2008, ISBN:
978-1405-16360-6. (Purchase
Here) |
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Seabra, G.M.,
Walker, R.C., Roitberg, A.E., "Quantifying Solvation
Effects on Peptide Conformations: A QM/MM Replica
Exchange Study.", in "Solvation Effects on
Molecules and Biomolecules: Computational Methods and
Applications (Challenges and Advances in Computational
Chemistry and Physics) ", Ed. Prof. Sylvio Canuto, Springer,
2008, ISBN: 978-1-4020-8269-6.
(Purchase
Here) |
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