Keck II Computing Facility: Publications

• Baldridge group
• Jennings group
• McCammon group
• Okamura group
• Onuchic group
• Perrin group
• Taylor group
• Wolynes group

Baldridge Group

• Wibke Sudholt, Kim K. Baldridge, David Abramson, Colin Enticott, Slavisa Garic, "Parameter Scan of an Effective Group Difference Pseudopotential Using Grid Computing", New Generation Computing (2004) 22, 137-146.
• W. Sudholt, K. K. Baldridge, D. Abramson, C. Enticott, S. Garic, "Applying grid computing to the parameter sweep of a group difference pseudopotential", in "Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part I", M. Bubak, G. D. van Albada, P. M. A. Sloot, J. J. Dongarra (Eds.), Springer-Verlag Heidelberg 2004, Lecture Notes in Computer Science 3036 (2004) 148-155

• Rodriguez J. C., Jennings P. A. amd Melacini G. Effect of Chemical Exchange on Radiation Damping in Aqueous Solutions of the Osmolyte Glycine. J. Amer. Chem. Soc. 124, 6240-6241 (2002).
• Hamuro, Y., Wong, L., Shaffer, J., Kim, J.S., Stranz, D.D., Jennings, P.A., Woods, V.L. Jr., and Adams, J.A. Phosphorylation driven motions in the COOH-terminal Src kinase, CSK, revealed through enhanced hydrogen-deuterium exchange and mass spectrometry (DXMS). J Mol Biol 323(5): 871-81 (2002).
• Roy, M and Jennings, P. A. Real-time NMR kinetic studies provide global and residue-specific information on the non-cooperative unfolding of the beta-trefoil protein, interleukin-1beta. J Mol Biol, 328(3), 693-703 (2003).
• Fayos, R., Melacini, G., Newlon, M. G., Burns, L., Scott, J. D., and Jennings, P. A. Induction of Flexibility through Protein-Protein Interactions. J Biol Chem, 278 (20), 18581-7 (2003).
• Wong, L., Jennings, P.A., and Adams, J.A. (2004). "Communication Pathways between the Nucleotide Pocket and Distal Regulatory Sites in Protein Kinases" Acc Chem Res 37, 304-311.
• Jiang, T., Olson, E. S., Nguyen, Q. T., Roy, M., Jennings, P. A. & Tsien, R. Y. (2004). Tumor imaging by means of proteolytic activation of cell-penetrating peptides. Proc Natl Acad Sci U S A 101, 17867-72.
• Rodriguez, J. C., Jennings, P. A. & Melacini, G. (2004). Using chemical exchange to assign non-covalent protein complexes in slow exchange with the free state: Enhanced resolution and efficient signal editing. J Biomol NMR 30, 155-61.
• Roy, M., Chavez, L. L., Finke, J. M., Heidary, D. K., Onuchic, J. N. & Jennings, P. A. (2005). The native energy landscape for Interleukin-1ß. Modulation of the population ensemble through native-state topology. J Mol Biol in press.
• Wong, L., Lieser, S., Chie-Leon, B., Miyashita, O., Aubol, B., Shaffer, J., Onuchic, J. N., Jennings, P. A., Woods, V. L., Jr., & Adams, J. A. (2004) Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk. J Mol Biol 341, 93-106.

• Baker, N.A., D. Sept, S. Joseph, M.J. Holst, J.A. McCammon. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 (2001).
• Tai, K., T. Shen, U. Borjesson, M. Philippopoulos, J.A. McCammon. Analysis of a Ten-nanosecond Molecular Dynamics Simulation of Mouse Acetylcholinesterase. Biophys. J. 81, 715-724 (2001).
• Sept, D., J.A. McCammon. Thermodynamics and Kinetics of Actin Filament Nucleation. Biophys. J. 81, 667-674 (2001).
• Ni, H., C.A. Sotriffer, J.A. McCammon. Ordered Water and Ligand Mobility in the HIV-1 Integrase - 5CITEP Complex: A Molecular Dynamics Study. J. Med. Chem. 44, 3043-3047 (2001).
• Ma, C., N.A. Baker, S. Joseph, J.A. McCammon. Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: A Continuum Electrostatics Investigation. J. Amer. Chem. Soc. 124, 1438-1442 (2002)
• Shen, T., K. Tai, R.H. Henchman, J.A. McCammon. Molecular Dynamics of Acetylcholinesterase. Acc. Chem. Res. 2002, 35, 332-340.
• N. A. Baker, J. A. McCammon. Electrostatic Interactions. In Structural Bioinformatics, H. Weissig and P. E. Bourne, eds. John Wiley and Sons: New York. To appear.
• N. Baker, K. Tai, R. Henchman, D. Sept, A. Elcock, M. Holst, J. A. McCammon Mathematics and Molecular Neurobiology. In Proceedings of the 3rd International Workshop on Methods for Macromolecular Modeling, New York City, October 12-14, 2000. New York: Springer-Verlag. To appear.
• N. A. Baker, D. Sept, M. J. Holst, and J. Andrew McCammon. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM Journal of Research and Development. 45, 427-438, 2001.
• J.-H. Lin, N. A. Baker, J. A. McCammon. Bridging implicit and explicit solvent approaches for membrane electrostatics, Biophys. J. in press (2002).
• Kaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot, J. Andrew McCammon. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J. Am. Chem. Soc. 2002, 124, 6153-6161.
• Lin, J.H., A. Perryman, J. Schames, J.A. McCammon. Computational Drug Design Accommodating Receptor Flexibility - The Relaxed Complex Scheme. J. Amer. Chem. Soc. 124, 5632-5633 (2002).
• Karplus, M., J.A. McCammon. Molecular Dynamics Simulations of Macromolecules: A Perspective. Nature Struct. Biol. in press (2002).
• Shen, T., L.S. Canino, J.A. McCammon. Unfolding Proteins under External Forces: A Solvable Model under the Self-consistent Pair Contact Probability Approximation. Phys. Rev. Letts. in press (2002).
• Kua, J., Y. Zhang, J.A. McCammon. Studying Enzyme Binding Specificity in Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach. J. Amer. Chem. Soc. in press (2002).
• Lin, J.H., A. Perryman, J. Schames, J.A. McCammon. The Relaxed Complex Method: Accomodating Receptor Flexibility for Drug Design with an Improved Scoring Scheme. Biopolymers 68, 47-62 (Kollman memorial issue, 2002).
• Podtelezhnikov, A.A., K. Gao, F.D. Bushman, J.A. McCammon. Modelling HIV-1 Integrase Complexes Based on their Hydrodynamic Properties. Biopolymers in press (Kollman memorial issue, 2002).
• Alexander L. Perryman and J. Andrew McCammon. AutoDocking Dinucleotides to the HIV-1 Integrase Core Domain: Exploring Possible Binding Sites for Viral and Genomic DNA J. Med. Chem. 45, 5624-5627 (2002).
• Wong, C.F., J.A. McCammon. Protein Flexibility and Computer-aided Drug Design. Annu. Rev. Pharmacol. Toxicol. 43, 31-45 (2003).
• Nielsen, J.E., J.A. McCammon. On the Evaluation and Optimisation of Protein X-ray Structures for pKa Calculations. Protein Sci. 12, 313-326 (2003).
• Zhang, Y., J.A. McCammon. Studying the Affinity and Kinetics of Molecular Association with Molecular Dynamics Simulation. J. Chem. Phys. 118, 1821-1827 (2003).
• Wong, C.F., J.A. McCammon. Protein Simulation and Drug Design. Adv. Protein Chem. 66, 87-121 (2003).
• Morikis, D., A.H. Elcock, P.A. Jennings, J.A. McCammon. The pH Dependence of Stability of the Activation Helix and the Catalytic Site of GART. Biophys. Chem. 105, 279-291 (2003).
• Shen, T., C.F. Wong, J.A. McCammon. Brownian Dynamics Simulation of Helix-capping Motifs. Biopolymers 70, 252-259 (2003).
• Toendel, K., C.F. Wong, J.A. McCammon. Computational Analysis of the Interactions between the Angiogenesis Inhibitor PD173074 and Fibroblast Growth Factor Receptor 1. J. Theor. Comp. Chem. 2, 43-56 (2003).
• Tai, K., S.D. Bond, H.R. MacMillan, N.A. Baker, M.J. Holst, J.A. McCammon. Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions. Biophys. J. 84, 2234-2241 (2003).
• Zhang, Y., J. Kua, J.A. McCammon. Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies. J. Phys. Chem. B 107, 4459 - 4463 (2003).
• Sims, P.A., C.F. Wong, J.A. McCammon. A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 Inhibitors. J. Med. Chem. 26, 3314-3325 (2003).
• Shi, J., K. Tai, J.A. McCammon, P. Taylor, D.A. Johnson. Nanosecond Dynamics of the Mouse Acetylcholinesterase Cys69-Cys96 Omega Loop. J. Biol. Chem. 278, 30905-30911 (2003).
• Puerta, D.T., J.R. Schames, R.H. Henchman, J.A. McCammon, S.M.Cohen. From Model Complexes to Metalloprotein Inhibition: A Synergistic Approach to Structure-based Drug Discovery. Angew. Chem. 42, 3772-3774 (2003).
• Nielsen, J.E., J.A. McCammon. Calculating pKa values in enzyme active sites. Protein Sci. 12, 1894-1901 (2003).
• Cerutti, D., C.F. Wong, J.A. McCammon. Brownian Dynamics Simulations of Ion Atmospheres around Polyalanine and B-DNA: Effects of Biomolecular Dielectric. Biopolymers 70, 391-402 (2003).
• Sept, D., N.A. Baker, J.A. McCammon. The Physical Basis of Microtubule Structure and Stability. Protein Science 12, 2257-2261 (2003).
• Bui, J., R.H. Henchman, J.A. McCammon. The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase Gorge. Biophys. J. 85, 2267-2272 (2003).
• Henchman, R.H., H.L.Wang, S.M. Sine, P. Taylor, J.A. McCammon. Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys. J. 85, 3007-3018 (2003).
• Kua, J., Y. Zhang, A.C. Eslami, J.R. Butler, J.A. McCammon. Studying the Roles of W86, E202, Y337 in Binding of Acetylcholine to Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach. Protein Sci. 12, 2675-2684 (2003).
• R. H. Henchman. Partition function for a simple liquid using cell theory parametrized by computer simulation. J. Chem. Phys. 119, 400-406 (2003).
• Vitalis, A., N.A. Baker, J.A. McCammon. ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules, Mol. Simul. 30, 45-61 (2004).
• Swanson, J.M.J., R.H. Henchman, J.A. McCammon. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy. Biophys. J. 86, 67-74 (2004).
• Trylska, J., P. Grochowski, J.A. McCammon. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. Protein Sci. 13, 513-528(2004).
• Song,Y., Y. Zhang, T. Shen, C.L. Bajaj, J.A. McCammon, N.A. Baker. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J. 86, 2017-2029 (2004).
• Trylska, J., R. Konecny, F. Tama, C.L.Brooks, J.A. McCammon. Ribosome Motions Modulate Electrostatic Properties. Biopolymers, 74(6), 423-431 (2004).
• Perryman, A., J.H. Lin, J.A. McCammon. HIV-1 Protease Molecular Dynamics of a Wild-Type and of the V82F/I84V Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for Drugs. Protein Sci. 13, 1108-1123 (2004).
• Zhang, D., R. Konecny, N.A. Baker, J.A. McCammon. Electrostatic Interaction between RNA and Protein Capsid in CCMV Simulated by a Coarse-grain RNA model and a Monte Carlo Approach. Biopolymers, 75(4), 325-337 (2004).
• R. H. Henchman, H. Wang, S. M. Sine, P. Taylor, J. A. McCammon. Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys. J., 2005, 88, 2564-2576
• Zhang, D., J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M.J. Holst, C. Bajaj, N.A. Baker, J.A. McCammon. Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods. Biophys. J. 88, 1659-1665 (2005).
• Dolinsky, T.J., J.E. Nielsen, J.A. McCammon, N.A. Baker. PDB2PQR: An Automated Pipeline for the Setup, Execution, and Analysis of Poisson-Boltzmann Electrostatics Calculations. Nucl. Acid Res. 32, W665-W669 (2004).
• Sims, P.A., C.F. Wong, J.A. McCammon. Charge Optimization of the Interface between Protein Kinases and their Ligands. J. Comp. Chem. 25, 1416-1429 (2004).
• Senapati, S., C.F. Wong, J.A. McCammon. Finite concentration effects on diffusion-controlled reactions. J. Chem. Phys. 121, 7896-7900 (2004).
• Cerutti, D.S., L.F. Ten Eyck, J.A. McCammon. Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. J. Chem. Theory Comput. 1, 143-152 (2005).
• Lu, B., C.F. Wong, J.A. McCammon. Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study. Protein Sci. 14, 159-168 (2005).
• Cheng, Y., Y. Zhang, J.A. McCammon. How does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: an ab initio QM/MM Study. J. Amer. Chem. Soc. 127, 1553-1562 (2005).
• Sims, P.A., C.F. Wong, D. Vuga, J.A. McCammon, B.M. Sefton. Relative Contributions of Desolvation, Inter- and Intramolecular Interactions to Binding Affinity in Protein Kinase Systems. J. Comp. Chem. 26, 668-681 (2005).

• Axelrod, H.L., Abresch, E.C., Okamura, M.Y., Yeh, A.P., Rees, D.C., and Feher, G. : X-ray structure determination of the cytochrome c2:reaction center electron transfer complex from Rhodobacter sphaeroides J. Mol. Biol. 319, 501-515 (2002).

• O. Miyashita, H. Axelrod and J. N. Onuchic; Different Scenarios for Inter-Protein Electron Tunneling; The Effect of Water-Mediated Pathways. Journal of Biological Physics, 2002. 28(3): p. 383-394.
• Miyashita, O.; Okamura, M. Y.; Onuchic, J. N.; Theoretical Understanding of the Interprotein Electron Transfer between Cytochrome c2 and the Photosynthetic Reaction Center J. Phys. Chem. B. ; 2003; 107(5); 1230-1241.
• Miyashita, O., J.N. Onuchic, and M.Y. Okamura, Continuum electrostatic model for the binding of cytochrome c(2) to the photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry, 2003. 42(40): p. 11651-11660.
• Miyashita, O., J.N. Onuchic, and P.G. Wolynes, Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A, 2003. 100(22): p. 12570-12575.
• M. S. Cheung, J. M. Finke, B. Callahan, J. N. Onuchic Exploring the interplay of topology and secondary structural formation in the protein folding problem. 2003. J. Phys. Chem., B, vol. 107. 11193-11200.
• A. M. Fernandez-Escamilla, M. S. Cheung, M. C. Vega, M. Wilmanns, J. N. Onuchic, L. Serrano Solvation in protein folding analysis, combination of theoretical and experimental approaches. 2004 Proceedings of the National Academy of Science . vol.101 2834-2839
• Leslie L. Chavez, Jose' N. Onuchic, and Cecilia Clementi. Quantifying the roughness on the Free Energy Landscape: Entropic bottlenecks and protein folding rates. J. Am. Chem. Soc, 126(27) pp 8426 - 8432, 2004.
• J. M. Finke, M. S. Cheung, J. N. Onuchic Modeling polyglutamine structure using a host-guest method combining Landscape Theory with experimental constraints 2004 Biophysical journal vol. 87 p1900-1918
• Yaakov Levy, Garegin A. Papoian, Jose' N. Onuchic, and Peter G. Wolynes, The energy landscape analysis of protein dimers Israel J. Chemistry, 44, 281-297, (2004)
• Yaakov Levy, Amedeo Caflisch, Jose' N. Onuchic, and Peter G. Wolynes, The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations, J. Mol. Biol., 340, 67-79, 2004.
• Sichun Yang, Samuel S. Cho, Yaakov Levy , Margaret S. Cheung, Herbert Levine, Peter G. Wolynes and Jose' N. Onuchic, Domain swapping is a consequence of minimal frustration, Proc. Natl. Acad. Sci. USA, 101, 13786-13791, (2004).
• Yaakov Levy, Samuel S. Cho, Tongye Shen, Jose' N. Onuchic, and Peter G Wolynes, Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery, Proc. Natl. Acad. Sci. USA, 102, 2373-2378, (2005).
• Yaakov Levy, Samuel S. Cho, Jose' N. Onuchic, and Peter G Wolynes, A survey of flxible protein binding mechanisms and their transition states using native topology based energy landscapes, J. Mol. Biol., 346, 1121-1145, (2005).
• Sichun Yang, H. Levine, and Jose' N. Onuchic, Protein oligomerization through domain swapping: Role of inter-molecular interactions and protein concentration, J. Mol. Biol. 352 (1) 202-211 (2005)

• Perrin, C. L.; Ohta, B. K.; Kuperman, J.; Liberman, J.; Erdélyi, M. "Stereochemistry of beta-Deuterium Isotope Effects on Amine Basicity", J. Am. Chem. Soc. 2005, 127, 9641-9647.

• Yang J, Ten Eyck LF, Xuong NH, Taylor SS. Crystal structure of a cAMP-dependent protein kinase mutant at 1.26A: new insights into the catalytic mechanism. J Mol Biol. 2004 Feb 13;336(2):473-87.

• Johan Ulander and A. D. J. Haymet : "Permeation Across Hydrated DPPC Lipid Bilayers: Simulation of the Titrable Amphiphilic Drug Valproic Acid" Biophysical Journal Volume 85 , December 2003 , 3475-3484.