Main     Research     Members     Publications     Links     Positions     Contact


Publications


Madej, B., Gould, I.R., Walker, R.C., "A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field", J. Phys. Chem. B., 2015, in press.

Hopkins C.W., Le Grand, S., Walker, R.C., Roitberg, A.E., "Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning", J. Chem. Theory. Comput., 2015, 11 (4), 1864-1874, DOI: 10.1021/ct5010406 (Full Text PDF)

Adhikary, R., Yu, W., Oda, M., Chen, T., Walker, R.C., Stanfield, R., Wilson, I., Zimmermann, J., Romesburg, F.E., "Adaptive mutations alter antibody structure and dynamics during affinity maturation", Biochemistry, 2015, 54 (11), 2085-2093, DOI: 10.1021/bi501417q (Full Text PDF)

Anandakrishnan, R., Drozdetski, A., Walker, R.C., Onufriev, A.V., "Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations", Biophysical Journal, 2015, 108, 1153-1164, DOI: 10.1016/j.bpj.2014.12.047 (Full Text PDF)

Skjevik, A.A., Madej, B.D., Dickson, C.J., Teigen, K., Gould, I.R., Walker, R.C., "All-Atom Lipid Bilayer Self-Assembly with the AMBER and Charmm Lipid Force Fields", Chemical Communications, 2015, 51, 4402, DOI: 10.1039/C4CC09584G (Full Text PDF, Supplemental Material)

Mones, L., Jones, A., Goetz, A.W., Laino, T., Walker, R.C., Leimkuhler, B., Csanyi, G., Bernstein, N., "The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.", J. Comput. Chem., 2015, 36, pp. 633-648, DOI: 10.1002/jcc.23839 (Full Text PDF)

Betz, R.M., Walker, R.C., "Paramfit: Automated optimization of force field parameters for molecular dynamics simulations", J. Comp. Chem, 2015, 36 (2), pp79-87, DOI: 10.1002/jcc.23775. (Full Text PDF, Cover Image)

Betz, R.M., Walker, R.C., "Streamlining Development of a Multimillion-Line Computational Chemistry Code", IEEE Computing in Science and Engineering, 2014, 9, 16 (3), pp10-17, DOI: 10.1109/MCSE.2014. (Full Text PDF)

Zhang, X., Walker, R.C., Phizicky, E., Mathews, D., "The influence of sequence and covalent modifications on yeast tRNA dynamics", J. Chem. Theory. Comput., 2014, 10 (8), pp3473-3483. DOI: 10.1021/ct500107y (Full Text PDF, Supplementary Material)

Yinglong, M., Sinko, W., Levi, P., Bucher, D., Walker, R.C., McCammon, J.M., "Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation", J. Chem. Theory Comput., 2014, 10 (7), pp 2677-2689, DOI: 10.1021/ct500090q (Full Text PDF)

Mendieta-Moreno, J.I., Walker, R.C., Lewis, J.P., Gomez-Puertas, P., Mendieta J., Ortega, J., "Fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems", J. Chem. Theory Comput., 2014, 10 (5), pp2185-2193, DOI: 10.1021/ct500033w,  (Full Text PDF)

Noodleman, L., Han Du, W., Fee, J., Goetz, A.W., Walker, R.C., "Linking Chemical Electron-Proton transfer to Proton Pumping in Cytochrome c Oxidase: Broken Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron-Copper Dinuclear Complex", Inorg. Chem., 2014, 53 (13), pp 6458-6472, DOI: 10.1021/ic500363h, (Full Text PDF, Supplemental Material 1,2,3)

Case, D.A., Walker, R.C. et al. AMBER 14, 2014, University of California, San Francisco.

Betz, R.M., DeBardeleben, N.A., Walker, R.C., "An Investigation of the effects of hard and soft errors on graphics processing unit-accelerated molecular dynamics simulations", Concurrency and Computation: Practice and Experience, 2014, DOI: 10.1002/cpe.3232 (Full Text PDF)

Dickson, C.J., Madej, B.D., Skjevik, A.A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., "Lipid14: The Amber Lipid Force Field", J. Chem. Theory Comput., 2014, 10(2), 865-879, DOI: 10.1021/ct4010307 (Full Text PDF, Supplemental Material)

Frank, M., Walker, R.C., Lanzilotta, W.N., Prestegard, J.H., Barb, A.W., "Immunoglobulin G1 Fc domain motions: implications for Fc engineering", J. Mol. Biol., 2014, 426(8), 1799-1811, DOI: 10.1016/j.jmb.2014.01.011 (Full Text PDF)

Goetz, A.W., Clark, M.A., Walker, R.C., "An extensible interface for QM/MM molecular dynamics simulations with AMBER.", J. Comput. Chem., 2014, 35, pp95-108 DOI: 10.1002/jcc.23444 (Full Text PDF, Supplemental Material, Cover Image)

Barkho, S., Pierce, L.C.T., McGlone, M.L., Li, S., Woods Jr, V.L., Walker, R.C., Adams, J.A., Jennings, P.A., "Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)", PLoS Comput Biol 2013, 9(9): e1003188. DOI: 10.1371/journal.pcbi.1003188

Salomon-Ferrer, R., Goetz, A.W., Poole, D., Le Grand, S., Walker, R.C., "Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald", J. Chem. Theory Comput., 2013, 9(9), pp3878-3888, DOI: 10.1021/ct400314y (Full Text PDF, Supplemental Material PDF Supplemental Material Tar)

Bastidas, A.C., Pierce, L.C., Walker, R.C., Johnson, D.A., Taylor, S.S., "Influence of N-Myristylation and Ligand Binding on the Flexibility of the Catalytic Subunit of Protein Kinase A", Biochemistry., 2013, 52 (37) pp6368-6379, DOI: 10.1021/bi400575k (Full Text PDF, Supplemental Material).

Betz, R.M., Walker, R.C., "An Investigation of the Effects of Error Correcting Code on GPU-accelerated Molecular Dynamics Simulations", XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013, DOI: 10.1145/2484762.2484774 (Full Text PDF)

Kaus, J.W., Pierce, L.T., Walker, R.C., McCammon, J.A., "Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package", J. Chem. Theory. Comput., 2013, 9 (9), pp 4131-4139, DOI: 10.1021/ct400340s (Full Text PDF, Supplemental Material)

Betz, R.M.; Walker, R.C; "Implementing Continuous Integration Software in an Established Computational Chemistry Software Package", IEEE SE-CSE 2013, San Francisco, USA.(Full Text PDF) - Awarded Best Paper.

Grand, S.L.; Goetz, A.W.; Walker, R.C.; "SPFP: Speed without compromise - a mixed precision model for GPU accelerated molecular dynamics simulations", Chem. Phys. Comm., 2013, 184, pp374-380, DOI: 10.1016/j.cpc.2012.09.022 (Full Text PDF)

Isborn, C.M.; Goetz, A.W.; Clark, M.A.; Walker, R.C.; Martinez, T.J.; "Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein", J. Chem. Theory Comput., 2012, 8 (12), pp. 5092-5106, DOI: 10.1021/ct3006826 (Full Text PDF, Supplemental Material)

Salomon-Ferrer, R.; Case, D.A.; Walker, R.C.; "An overview of the Amber biomolecular simulation package", WIREs Comput. Mol. Sci., 2012, 3, pp198-210, DOI: 10.1002/wcms.1121 (Full Text PDF)

Skjevik, A.A,; Madej. B.D.; Walker, R.C.; Teigen, K.; "LIPID11: A Modular Framework for Lipid Simulations Using Amber", Journal of Physical Chemistry B, 2012, 116 (36), pp 11124-11136, DOI: 10.1021/jp3059992 (Full Text PDF, Supplemental Material)

Dickson, C.J.; Rosso, L.; Betz, R.M.; Walker, R.C.; Gould, I.R., "GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid.", Soft Matter, 2012, 8, 9617-9627, DOI: 10.1039/C2SM26007G (Full Text PDF, Supplemental Material)

Pierce, L.C.T., Salomon-Ferrer, R. de Oliveira, C.A.F. McCammon, J.A. Walker, R.C., "Routine access to millisecond timescale events with accelerated molecular dynamics.", Journal of Chemical Theory and Computation, 2012, 8 (9), pp 2997-3002, DOI: 10.1021/ct300284c

Park, K.; Goetz, A.W.; Walker, R.C.; Paesani, F., "Adaptive QM/MM molecular dynamics simulations of aqueous systems.", Journal of Chemical Theory and Computation, 2012, 8 (8), pp 2868-2877, DOI: 10.1021/ct300331f (Full Text PDF)

Votapka, L., Ozlem, D., Swift, R.V., Walker, R.C.,Amaro, R., "Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase.", J. Mol. Genet. Med., 2012, 6, 293-300 (Full Text PDF)

Goetz, A.W., Williamson, M.J., Xu, D., Poole, D.,Grand, S.L., Walker, R.C. "Routine microsecond molecular dynamics simulations with amber - part i: Generalized born", Journal of Chemical Theory and Computation, 2012, 8 (5), pp 1542-1555, DOI:10.1021/ct200909j (Full Text PDF)

Case, D.A., Walker, R.C. et al. AMBER 12, 2012, University of California, San Francisco.

Dodson, M.L., Walker, R.C., Lloyd, R.S., "Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site", PLoS ONE 2012, 7(2): e31377. doi:10.1371/journal.pone.0031377 (Full Text PDF)

Amaro, R.E., Swift, R.V., Votapka, L., Li, W.W., Walker, R.C., Bush, R.M., "Mechanism of 150-cavity formation in influenza neuraminidase", Nature: Communications, 2011, 2:388 doi: 10.1038/ncomms1390. (Full Text PDF)

Case, D.A., Walker, R.C. et al. AMBER 11, 2010, University of California, San Francisco.

Goetz, A.W., Woelfe, T., Walker, R.C., "Quantum Chemistry on Graphics Processing Units", Ann. Rep. Comp. Chem., vol 6. 2010, 21-35 (Chapter 2). (Full Text PDF)

Xu, D., Williamson, M.J., Walker, R.C., "Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units.", Ann. Rep. Comp. Chem., vol 6. 2010, 2-19 (Chapter 1). (Full Text PDF)

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, 78, 2523-2532 (Full Text PDF)

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)

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)

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)

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)

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)

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)

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)

Case, D.A., Walker, R.C. et al. AMBER 10, 2008, University of California, San Francisco.

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)

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)

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)

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)

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)

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)

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)

Case, D.A., Walker, R.C. et al. AMBER 9, 2006, University of California, San Francisco.

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)

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.

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.

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)

 

Collected Works

 


Bhuiyan, A., Needham, P., Walker, R.C., "Amber PME Molecular Dynamics Optimization", ed. Jeffers, J., Reinders, J., in High Performance Parallelism Pearls Volume Two: Multicore and Many-core Programming Approaches, 2015, ISBN 978-0128038192 (Purchase Here)

Nurisso, A., Daina, A., Walker, R.C., "A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling", Ed. A. Orry, Springer, Methods in Molecular Biology Series, 2012, vol 857, ISBN 978-1-61779-587-9 (Purchase Here)

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 (Purchase Here)

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)

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)

 

 


the Walker Molecular Dynamics lab