Publications 2005 - 2009

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  1. Henchman, R.H., J.A. McCammon. Protein structural flexibility: molecular motions. In "Encyclopedia of Life Sciences," John Wiley and Nature Publishing Group (2005).
  2. McCammon, J.A. Computation of Non-covalent Binding Affinities. In "Theory and Applications of Computational Chemistry," C. Dykstra, G. Frenking, K. Kim, and G. Scuseria, Eds., Elsevier, Amsterdam, Ch. 3, pp. 41-46 (2005).
  3. 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).
  4. 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). [PubMed]
  5. Hamelberg, D., T. Shen, J.A. McCammon. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: Accelerated molecular dynamics analysis. J. Amer. Chem. Soc. 127, 1969-1974 (2005). [PubMed]
  6. 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). [PubMed]
  7. Henchman, R.H., H.-L. Wang, S.M. Sine, P. Taylor, J.A. McCammon. Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain. Biophys. J. 88, 2564-2576 (2005). [PubMed]
  8. Gao, F., N. Bren, T.P. Burghardt, S. Hansen, R.H. Henchman, P. Taylor, J.A. McCammon, S.M. Sine. Agonist-mediated conformational changes in ACh-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J. Biol. Chem. 280, 8443-8451 (2005). [PubMed]
  9. Zhang, D., J. Suen, Y. Zhang, Y. Song, Z. Radić, 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). [PubMed]
  10. 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. Comput. Chem. 26, 668-681 (2005). [PubMed]
  11. Bui, J.M., J.A. McCammon. Acetylcholinesterase: Pivotal Roles of its Long Omega Loop (Cys69-Cys96) in Regulating Binding. Chem.-Biol. Interact. Vol. 157-158, 357-359 (2005). [PubMed]
  12. Law, R.J., R.H. Henchman, J.A. McCammon. A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. USA 102, 6813-6818 (2005). [PubMed]
  13. Dzubiella, J., J.A. McCammon. Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J. Chem. Phys. 122, article 184902 (2005). [PubMed]
  14. McCammon, J.A., R.C. Wade. Pushing the limits: Editorial overview. Curr. Opin. Struct. Biol. 15, 135-136 (2005).
  15. Swanson, J.M.J., S.A. Adcock, J.A. McCammon. Optimized radii for Poisson-Boltzmann calculations with the AMBER force field. J. Chem. Theory Comput. 1, 484-493 (2005).
  16. Lu, B., D. Zhang, J.A. McCammon. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J. Chem. Phys. 122, article 214102 (2005). [PubMed]
  17. Shen, T., C. Zong, D. Hamelberg, J.A. McCammon, P.G. Wolynes. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. The FASEB J. 19, 1389-1395 (2005). [PubMed]
  18. Hamelberg, D., T. Shen, J.A. McCammon. Relating kinetic rates and local energetic roughness by accelerated molecular dynamics simulations. J. Chem. Phys. 122, article 241103 (2005).
  19. Trylska, J., V. Tozzini, J.A. McCammon. Exploring Global Motions and Correlations in the Ribosome. Biophys. J. 89, 1455-1463 (2005). [PubMed]
  20. Tozzini, V., J.A. McCammon. A coarse grained model for the dynamics of the early stages of the binding mechanism of HIV-1 Protease. Chem. Phys. Letters 413, 123-128 (2005).
  21. Trylska, J., J.A. McCammon, C.L. Brooks III. Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach. J. Amer. Chem. Soc. 127, 11125-11133 (2005). [PubMed]
  22. Wong, C.F., J. Kua, Y. Zhang, T.P. Straatsma, J.A. McCammon. Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase A. Proteins: Str. Fn. Bioinf. 61, 850-858 (2005). [PubMed]
  23. Minh, D.D.L., J.M. Bui, C. Chang, T. Jain, J.M.J. Swanson, J.A. McCammon. The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2. Biophys. J. 89, L25-L27 (2005). [PubMed]
  24. Swanson, J.M.J., J. Mongan, J.A. McCammon. Limitations of Atom-Centered Dielectric Functions in Implicit Solvent Models. J. Phys. Chem. B 109, 14769-14772 (2005). [PubMed]
  25. Lu, B., X. Cheng, T. Hou, J.A. McCammon. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J. Chem. Phys. 123, article 084904 (2005). [PubMed]
  26. McCammon, J.A. Target Flexibility in Molecular Recognition. Bioch. Biophys. Acta 1754, 221-224 (2005, Special issue on Inhibitors of Protein Kinases). [PubMed]
  27. Hamelberg, D., J.A. McCammon. Fast Peptidyl cis-trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease. J. Amer. Chem. Soc. 127, 13778-13779 (2005). [PubMed]
  28. Puerta, D.T., J. Mongan, B.L. Tran, J.A. McCammon, S.M. Cohen. Potent, Selective Pyrone-Based Inhibitors of Stromelysin-1. J. Amer. Chem. Soc. 127, 14148-14149 (2005). [PubMed]
  29. Senapati, S., J.M. Bui, J.A. McCammon. Induced Fit in Mouse Acetylcholinesterase upon Binding a Femtomolar Inhibitor: A Molecular Dynamics Study. J. Med. Chem. 48, 8155-8162 (2005). [PubMed]
  30. Zhang, D., J.A. McCammon. The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput. Biol. 1, 484-491 (2005). [PubMed]
  31. Gullingsrud, J., C. Kim, S.S. Taylor, J.A. McCammon. Dynamic binding of PKA regulatory subunit RIα. Structure 14, 141-149 (2006). [PubMed]
  32. Adcock, S.A., J.A. McCammon. Molecular Dynamics: A Survey of Methods for Simulating the Activity of Proteins. Chem. Revs. 106, 1589-1615 (2006). [PubMed]
  33. Cheng, X., B. Lu, B. Grant, R.J. Law, J.A. McCammon. Channel Opening Motion of α7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis. J. Mol. Biol. 355, 310-324 (2006). [PubMed]
  34. Perryman, A.L., J.-H. Lin, J.A. McCammon. Restrained Molecular Dynamics Simulations of HIV-1 Protease: Validating a New Target for Drug Design. Biopolymers 82, 272-284 (2006). [PubMed]
  35. Giorgione, J.R., J.-H. Lin, J.A. McCammon, A.C. Newton. Increased Membrane Affinity of the C1 Domain of Protein Kinase Cδ Compensates for the Lack of Involvement of its C2 Domain in Membrane Recruitment. J. Biol. Chem. 281, 1660-1669 (2006). [PubMed]
  36. Konecny, R., J. Trylska, F. Tama, D. Zhang, N.A. Baker, C.L. Brooks III, J.A. McCammon. Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus Capsids. Biopolymers 82, 106-120 (2006). [PubMed]
  37. Bui, J.M., Z. Radić, P. Taylor, J.A. McCammon. Conformational Transitions in Protein-Protein Association: Binding of Fasciculin-2 to Acetylcholinesterase. Biophys. J. 90, 3280-3287 (2006). [PubMed]
  38. Ung, M.-U., B. Lu, J.A. McCammon. E230Q Mutation of the Catalytic Subunit of cAMP-dependent Protein Kinase Affects Local Structure and the Binding of Peptide Inhibitor. Biopolymers 81, 428-439 (2006). [PubMed]
  39. Vigil, D., J.-H. Lin, C.A. Sotriffer, J.K. Pennypacker, J.A. McCammon, S.S. Taylor. A Simple Electrostatic Switch Important in the Activation of Type I Protein Kinase A By Cyclic AMP. Protein Sci. 15, 113-121 (2006). [PubMed]
  40. Hamacher, K., J. Trylska, J.A. McCammon. Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol. 2, 80-87 (2006). [PubMed]
  41. Dzubiella, J., J.M.J. Swanson, J.A. McCammon. Coupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent models. Phys. Rev. Letters 96, article 087802 (2006). [PubMed]
  42. Cheng, Y., Y. Zhang, J.A. McCammon. How does Activation Loop Phosphorylation Modulate Catalytic Activity in the cAMP-dependent Protein Kinase: A Theoretical Study. Protein Sci. 15, 672-683 (2006). [PubMed]
  43. Ivanov, I., S. Vemparala, V. Pophristic, K. Kuroda, W.F. DeGrado, J.A. McCammon, M.L. Klein. Characterization of Nonbiological Antimicrobial Polymers in Aqueous Solution and at Water-Lipid Interfaces from All-Atom Molecular Dynamics. J. Amer. Chem. Soc. 128, 1778-1779 (2006). [PubMed]
  44. Dzubiella, J., J.M.J. Swanson, J.A. McCammon. Coupling nonpolar and polar solvation free energies in implicit solvent models. J. Chem. Phys. 124, article 084905 (2006). [PubMed]
  45. Zhang, D., J. Gullingsrud, J.A. McCammon. Potentials of Mean Force for Acetylcholine Unbinding from the α7 Nicotinic Acetylcholine Receptor Ligand-Binding Domain. J. Amer. Chem. Soc. 128, 3019-3026 (2006). [PubMed]
  46. Chang, C.-E., T. Shen, J. Trylska, V. Tozzini, J.A. McCammon. Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Course-Grained Model. Biophys. J. 90, 3880-3885 (2006). [PubMed]
  47. Hamacher, K., A. Hübsch, J.A. McCammon. A Minimal Model for Stabilization of Biomolecules by Hydrocarbon Cross-linking. J. Chem. Phys. 124, article 164907 (2006). [PubMed]
  48. Tozzini, V., W. Rocchia, J.A. McCammon. Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide Model. J. Chem. Theory Comput. 2, 667-673 (2006). [PubMed]
  49. Shen, T., D. Hamelberg, J.A. McCammon. Elasticity of peptide omega bonds. Phys. Rev. E 73, article 041908 (2006). [PubMed]
  50. Hamacher, K., J.A. McCammon. Computing the amino acid specificity of fluctuations in biomolecular systems. J. Chem. Theory Comput. 2, 873-878 (2006).
  51. Hamelberg, D., J.A. McCammon. Accelerating Conformational Transitions in Biomolecular Systems. Annual Reports in Comput. Chem. 2, 221-232 (2006).
  52. Minh, D.D.L., C.-E. Chang, J. Trylska, V. Tozzini, J.A. McCammon. The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics. J. Amer. Chem. Soc. 128, 6006-6007 (2006). [PubMed]
  53. Cerutti, D.S., T. Jain, J.A. McCammon. CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci. 15, 1579-1596 (2006). [PubMed]
  54. Perryman, A.L., J.-H. Lin, J.A. McCammon. Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug-resistant Mutant of HIV-1 Protease: an Application of the Relaxed Complex Method of Structure-based Drug Design. Chem. Biol. & Drug Des. 67, 336-345 (2006).
  55. Gullingsrud, J., A. Babakhani, J.A. McCammon. Computational investigation of pressure profiles in lipid bilayers with embedded proteins. Mol. Sim. 32, 831-838 (2006).
  56. Lewis, J.A., J. Mongan, J.A. McCammon, S.M. Cohen. Evaluation and Binding Mode Prediction of Thiopyrone-Based Inhibitors of Anthrax Lethal Factor. ChemMedChem 1, 694-697 (2006). [PubMed]
  57. Jain, T., D.S. Cerutti, J.A. McCammon. Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci. 15, 2029-2039 (2006). [PubMed]
  58. Hamelberg, D., T. Shen, J.A. McCammon. Insight into the role of hydration on protein dynamics. J. Chem. Phys. 125, article 094905 (2006). [PubMed]
  59. Yang, G., J. Trylska, Y. Tor, J.A. McCammon. Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-Site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation, and Fluorescence Studies. J. Med. Chem. 49, 5478-5490 (2006). [PubMed]
  60. Grant, B.J., A.P.C. Rodrigues, K.M. ElSawy, J.A. McCammon, L.S.D. Caves. Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics 22, 2695-2696 (2006). [PubMed]
  61. Cheng, X., H. Wang, B. Grant, S.M. Sine, J.A. McCammon. Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors. PLoS Comput. Biol. 2, 1173-1184 (2006). [PubMed]
  62. Senapati, S., Y. Cheng, J.A. McCammon. In-situ synthesis of an inhibitor of acetylcholinesterase: Configurational selection imposed by steric interactions. J. Med. Chem. 49, 6222-6230 (2006). [PubMed]
  63. Bui, J.M., J.A. McCammon. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc. Natl. Acad. Sci. USA 103, 15451-15456 (2006). [PubMed]
  64. de Oliveira, C.A.F., D. Hamelberg, J.A. McCammon. On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations. J. Phys. Chem. B 110, 22695-22701 (2006). [PubMed]
  65. Ivanov, I., B.R. Chapados, J.A. McCammon, J.A. Tainer. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res. 34, 6023-6033 (2006). [PubMed]
  66. Lu, B., X. Cheng, J. Huang, J.A. McCammon. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc. Natl. Acad. Sci. USA 103, 19314-19319 (2006). [PubMed]
  67. Tozzini, V., J. Trylska, C. Chang, J.A. McCammon. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J. Struct. Biol. 157, 606-615 (2007). [PubMed]
  68. Swanson, J.M.J., J.A. Wagoner, N.A. Baker, J.A. McCammon. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. J. Chem. Theory Comput. 3, 170-183 (2007).
  69. Mongan, J., C. Simmerling, J.A. McCammon, D.A. Case, A. Onufriev. Generalized Born model with a simple, robust molecular volume correction. J. Chem. Theory Comput. 3, 156-169 (2007). [PubMed]
  70. Ivanov, I., J.A. Tainer, J.A. McCammon. Unraveling the Three-Metal-Ion Catalytic Mechanism of the DNA Repair Enzyme Endonuclease IV. Proc. Natl. Acad. Sci. USA 104, 1465-1470 (2007). [PubMed]
  71. LeDuc, P.R., M.S. Wong, P.M. Ferreira, R.E. Groff, K. Haslinger, M.P. Koonce, W.Y. Lee, J.C. Love, J.A. McCammon, N.A. Monteiro-Riviere, V.M. Rotello, G.W. Rubloff, R. Westervelt, M. Yoda. Towards an in vivo biologically inspired nanofactory. Nature Nanotech. 2, 3-7 (2007). [PubMed]
  72. Ngo, J.C.K., J. Gullingsrud, K. Giang, M.J. Yeh, X.-D. Fu, J.A. Adams, J.A. McCammon, G. Ghosh. SR protein kinase 1 is resilient to inactivation. Structure 15, 123-133 (2007). [PubMed]
  73. Chang, C.A., J. Trylska, V. Tozzini, J.A. McCammon. Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations. Chem. Biol. & Drug Des. 69, 5-13 (2007). [PubMed]
  74. Trylska, J., V. Tozzini, C.A. Chang, J.A. McCammon. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys. J. 92, 4179-4187 (2007). [PubMed]
  75. Gorfe, A.A., M. Hanzal-Bayer, D. Abankwa, J.F. Hancock, J.A. McCammon. Structure and Dynamics of the Full-Length Lipid-Modified H-Ras Protein in a 1,2-dimyristoylglycero-3-phosphocholine Bilayer. J. Med. Chem. 50, 674-684 (2007). [PubMed]
  76. Cheng, Y., J.K. Suen, Z. Radić, S.D. Bond, M.J. Holst, J.A. McCammon. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys. Chem. 127, 129-139 (2007). [PubMed]
  77. Cheng, Y., J.K. Suen, D. Zhang, S.D. Bond, Y. Zhang, Y. Song, N.A. Baker, C.L. Bajaj, M.J. Holst, J.A. McCammon. Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations. Biophys. J. 92, 3397-3406 (2007). [PubMed]
  78. Babakhani, A., A.A. Gorfe, J. Gullingsrud, J.E. Kim, J.A. McCammon. Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulation. Biopolymers 85, 490-497 (2007).
  79. Sørensen, J., D. Hamelberg, B. Schiøtt, J.A. McCammon. Comparative MD analysis of the stability of Transthyretin providing insight into the fibrillation mechanism. Biopolymers 86, 73-82 (2007). [PubMed]
  80. Grant, B.J., J.A. McCammon, L.S.D. Caves, R.A. Cross. Multivariate analysis of conserved sequence-structure relationships in kinesins: Coupling of the active site and a tubulin-binding domain. J. Mol. Biol. 368, 1231-1248 (2007). [PubMed]
  81. de Oliveira, C.A.F., M. Zissen, J. Mongan, J.A. McCammon. Molecular Dynamics Simulations of Metalloproteinases types 2 and 3 Reveal Differences in the Dynamic Behavior of the S1' Binding Pocket. Curr. Pharm. Des. 13, 3471-3475 (2007). [PubMed]
  82. Lu, B., J.A. McCammon. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. J. Chem. Theory Comput. 3, 1134-1142 (2007).
  83. Cheng, Y., X. Cheng, Z. Radić, J.A. McCammon. Acetylcholinesterase: Mechanisms of Covalent Inhibition of Wild-Type and H447I Mutant Determined by Computational Analyses. J. Amer. Chem. Soc. 129, 6562-6570 (2007). [PubMed]
  84. Ivanov, I., X. Cheng, S.M. Sine, J.A. McCammon. Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop Family. J. Amer. Chem. Soc. 129, 8217-8224 (2007). [PubMed]
  85. Hamelberg, D., J.A. McCammon. Dealing with bound waters in a site: Do they leave or stay? In "Computational and Structural Approaches to Drug Discovery," R.M. Stroud, Ed., Royal Society of Chemistry, Ch. 5, pp. 95-110 (2007).
  86. Amaro, R.E., D.D.L. Minh, L.S. Cheng, W.M. Lindstrom, Jr., A.J. Olson, J.-H. Lin, W.W. Li, J.A. McCammon. Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antiviral Drug Design. J. Amer. Chem. Soc. 129, 7764-7765 (2007). [PubMed]
  87. Lu, B., X. Cheng, J.A. McCammon. “New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems. J. Comput. Phys. 226, 1348-1366 (2007). [PubMed]
  88. Cheng, L.-T., J. Dzubiella, J.A. McCammon, B. Li. Application of the level-set method to the implicit solvation of nonpolar molecules. J. Chem. Phys. 127, article 084503 (2007). [PubMed]
  89. Cheng, X., I. Ivanov, H. Wang, S.M. Sine, J.A. McCammon. Nanosecond-Timescale Conformational Dynamics of the Human α7 Nicotinic Acetylcholine Receptor. Biophys. J. 93, 2622-2634 (2007). [PubMed]
  90. Amaro, R.E., R.V. Swift, J.A. McCammon. Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei. PLoS Negl. Trop. Dis. 1, e68 (2007). [PubMed]
  91. Gorfe, A.A., A. Babakhani, J.A. McCammon. Free Energy Profile of H-ras Membrane Anchor upon Membrane Insertion. Angew. Chem. Int. Ed. 46, 8234-8237 (2007). [PubMed]
  92. Khavrutskii, I.V., J.A. McCammon. Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints. J. Chem. Phys. 127, article 124901 (2007). [PubMed]
  93. Cerutti, D.S., N.A. Baker, J.A. McCammon. Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? J. Chem. Phys. 127, article 155101 (2007). [PubMed]
  94. Gorfe, A.A., A. Babakhani, J.A. McCammon. H-ras Protein in a Bilayer: Interaction and Structure Perturbation. J. Amer. Chem. Soc. 129, 12280-12286 (2007). [PubMed]
  95. Hamelberg, D., T. Shen, J.A. McCammon. A proposed signaling motif for nuclear import in mRNA processing via the formation of Arginine Claw. Proc. Natl. Acad. Sci. USA 104, 14947-14951 (2007). [PubMed]
  96. Lu, B., Y.C. Zhou, G.A. Huber, S.D. Bond, M.J. Holst, J.A. McCammon. Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J. Chem. Phys. 127, article 135102 (2007). [PubMed]
  97. Baron, R., J.A. McCammon. Dynamics, Hydration, and Motional Averaging of a Loop-Gated Artificial Protein Cavity: The W191G Mutant of Cytochrome c Peroxidase in Water as Revealed by Molecular Dynamics Simulations. Biochemistry 46, 10629-10642 (2007). [PubMed]
  98. Hamelberg, D., C.A.F. de Oliveira, J.A. McCammon. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J. Chem. Phys. 127, article 155102 (2007). [PubMed]
  99. de Oliveira, C.A.F., D. Hamelberg, J.A. McCammon. Estimating Kinetic Rates from Accelerated Molecular Dynamics Simulations: Alanine Dipeptide in Explicit Solvent as a Case Study. J. Chem. Phys. 127, article 175105 (2007). [PubMed]
  100. Minh, D.D.L., D. Hamelberg, J.A. McCammon. Accelerated entropy estimates with accelerated dynamics. J. Chem. Phys. 127, article 154105 (2007). [PubMed]
  101. Zhou, Y.C., M. Holst, J.A. McCammon. A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces. J. Math. Anal. Appl. 340, 135-164 (2008). [PubMed]
  102. Minh, D.D.L., J.A. McCammon. Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments. J. Phys. Chem. B 112, 5892-5897 (2008, A. Szabo festschrift). [PubMed]
  103. Zhou, Y.C., B. Lu, G.A. Huber, M.J. Holst, J.A. McCammon. Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A Poisson-Nernst-Planck Approach. J. Phys. Chem. B 112, 270-275 (2008, Casey Hynes festschrift). [PubMed]
  104. Gorfe, A.A., C.A. Chang, I. Ivanov, J.A. McCammon. Dynamics of the Acetylcholinesterase Tetramer. Biophys. J. 94, 1144-1154 (2008). [PubMed]
  105. Khavrutskii, I.V., J. Dzubiella, J.A. McCammon. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. J. Chem. Phys. 128, article 044106 (2008). [PubMed]
  106. Lu, B., J.A. McCammon. Molecular surface-free continuum model for electrodiffusion processes. Chem. Phys. Letters 451, 282-286 (2008). [PubMed]
  107. Amaro, R.E., R. Baron, J.A. McCammon. An Improved Relaxed Complex Scheme for Receptor Flexibility in Computer-Aided Drug Design. J. Comput.-Aided Mol. Des. 22, 693-705 (2008). [PubMed]
  108. Landon, M.R., R.E. Amaro, R. Baron, C.H. Ngan, D. Ozonoff, J.A. McCammon, S. Vajda. Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble. Chem. Biol. & Drug Des. 71, 106-116 (2008). [PubMed]
  109. Che, J., J. Dzubiella, B. Li, J.A. McCammon. Electrostatic Free Energy and its Variations in Implicit Solvent Models. J. Phys. Chem. B 112, 3058-3069 (2008). [PubMed]
  110. Wang, H.-L., X. Cheng, P. Taylor, J.A. McCammon, S.M. Sine. Control of cation permeation through the nicotinic receptor channel. PLoS Comput. Biol. 4, e41 (2008). [PubMed]
  111. Lu, B.Z., Y.C. Zhou, M.J. Holst, J.A. McCammon. Recent Progress in Numerical Methods for the Poisson-Boltzmann Equation in Biophysical Applications. Commun. Comput. Phys. 3, 973-1009 (2008).
  112. Abankwa, D., M. Hanzal-Bayer, N. Ariotti, S.J. Plowman, A.A. Gorfe, R.G. Parton, J.A. McCammon, J.F. Hancock. A novel switch region regulates H-ras membrane orientation and signal output. EMBO J. 27, 727-735 (2008). [PubMed]
  113. Gunatilleke, S.S., C.A.F. de Oliveira, J.A. McCammon, A.M. Barrios. Inhibition of Cathepsin B by Au(I) Complexes: A Kinetic and Computational Study. J. Biol. Inorg. Chem. 13, 555-561 (2008). [PubMed]
  114. Yu, Z., M.J. Holst, Y. Cheng, J.A. McCammon. Feature-Preserving Adaptive Mesh Generation for Molecular Shape Modeling and Simulation. J. Mol. Graph. Model. 26, 1370-1380 (2008). [PubMed]
  115. Swift, R.V., J.A. McCammon. Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics. Biochemistry 47, 4102-4111 (2008). [PubMed]
  116. Baron, R., J.A. McCammon. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. ChemPhysChem 9, 983-988 (2008). [PubMed]
  117. McCammon, J.A. Computer-aided Drug Discovery: Physics-based Simulations from the Molecular to the Cellular Level. In "Physical Biology: From Atoms to Medicine," A.H. Zewail, Ed., World Scientific Publishing, Ch. 16, pp. 401-410 (2008).
  118. Gorfe, A.A., B.J. Grant, J.A. McCammon. Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins. Structure 16, 885-896 (2008). [PubMed]
  119. Bui, J.M., J.A. McCammon. Intrinsic Conformational Flexibility of Acetylcholinesterase. Chem.-Biol. Interact. 175, 303-304 (2008).
  120. Chang, C.A., W.A. McLaughlin, R. Baron, W. Wang, J.A. McCammon. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc. Natl. Acad. Sci. USA 105, 7456-7461 (2008). [PubMed]
  121. Yu, Z., M.J. Holst, J.A. McCammon. High-fidelity geometric modeling for biomedical applications. Finite Elements in Analysis and Des. 44, 715-723 (2008).
  122. Cheng, L.S., R.E. Amaro, D. Xu, W.W. Li, P.W. Arzberger, J.A. McCammon. Ensemble-based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase. J. Med. Chem. 51, 3878-3894 (2008). [PubMed]
  123. Tozzini, V., J.A. McCammon. One-Bead Coarse-Grained Models for Proteins. In "Coarse-graining of Condensed Phase and Biomolecular Systems," G.A. Voth, Ed., CRC Press, Ch. 19, pp. 285-298 (2008).
  124. Cheng, Y.H., X.L. Cheng, Z. Radić, J.A. McCammon. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chem.-Biol. Interact. 175, 196-199 (2008). [PubMed]
  125. Wong, S.E., R. Baron, J.A. McCammon. Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. Biopolymers 89, 916-920 (2008). [PubMed]
  126. Gorfe, A.A., R. Baron, J.A. McCammon. Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven hydrophobic effect. Biophys. J. 95, 3269-3277 (2008). [PubMed]
  127. Khavrutskii, I.V., M. Fajer, J.A. McCammon. Intrinsic free energy of the conformational transition of the KcsA signature peptide from conducting to non-conducting state. J. Chem. Theory Comput. 4, 1541-1554 (2008). [PubMed]
  128. Babakhani, A., A.A. Gorfe, J.E. Kim, J.A. McCammon. Thermodynamics of Peptide Insertion and Aggregation in a Lipid Bilayer. J. Phys. Chem. B 112, 10528-10534 (2008). [PubMed]
  129. de Oliveira, C.A.F., D. Hamelberg, J.A. McCammon. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. J. Chem. Theory Comput. 4, 1516-1525 (2008). [PubMed]
  130. Mura, C., J.A. McCammon. Molecular dynamics of a κB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res. 36, 4941-4955 (2008). [PubMed]
  131. Fajer, M., D. Hamelberg, J.A. McCammon. Replica Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J. Chem. Theory Comput. 4, 1565-1569 (2008). [PubMed]
  132. Gorfe, A.A., J.A. McCammon. Similar Membrane Affinity of Mono- and Di-S-acylated Ras Membrane Anchors: A New Twist in the Role of Protein Lipidation. J. Amer. Chem. Soc. 130, 12624-12625 (2008). [PubMed]
  133. Cheng, Y., C.A. Chang, Z. Yu, Y. Zhang, M. Sun, T.S. Leyh, M.J. Holst, J.A. McCammon. Diffusional Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-grained Brownian Dynamics Studies. Biophys. J. 95, 4659-4667 (2008). [PubMed]
  134. Baron, R., S.E. Wong, C.A.F. de Oliveira, J.A. McCammon. E9-Im9 Colicin DNase-Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study. J. Phys. Chem. B 112, 16802-16814 (2008). [PubMed]
  135. Yu, Z., M.J. Holst, T. Hayashi, C.L. Bajaj, M.H. Ellisman, J.A. McCammon, M. Hoshijima. Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation. J. Struct. Biol. 164, 304-313 (2008). [PubMed]
  136. Amaro, R.E., A. Schnaufer, H. Interthal, W. Hol, K.D. Stuart, J.A. McCammon. Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 105, 17278-17283 (2008). [PubMed]
  137. Hamelberg, D., J.A. McCammon. Mechanistic insight into the role of transition state stabilization in Cyclophilin A. J. Amer. Chem. Soc. 131, 147-152 (2009). [PubMed]
  138. Lu, S., A.P. Michailova, J.J. Saucerman, Y. Cheng, Z. Yu, T.H. Kaiser, W.W. Li, R.E. Bank, M.J. Holst, J.A. McCammon, T. Hayashi, M. Hoshijima, P. Arzberger, A.D. McCulloch. Multi-Scale Modeling of Ventricular Myocytes: Contributions of structural and functional heterogeneities to excitation-contraction coupling in the normal and failing rodent heart. IEEE Eng. Med. Biol. 28, 46-57 (2009).
  139. Baker, N.A., J.A. McCammon. Electrostatic Interactions. In "Structural Bioinformatics," Second Edition, P.E. Bourne and J. Gu, Eds., John Wiley & Sons, New York, pp. 575-592 (2009).
  140. McCammon, J.A. Computational Studies of Protein Dynamics. In "Water and Biomolecules - Physical Chemistry of Life Phenomena," K. Kuwajima, et al., Eds., Springer, New York, Ch. 11, pp. 211-218 (2009).
  141. Williams, S.L., J.A. McCammon. Conformational Dynamics of the Flexible Catalytic Loop in Mycobacterium tuberculosis 1-Deoxy-D-xylulose 5-Phosphate Reductoisomerase. Chem. Biol. & Drug Des. 73, 26-38 (2009).
  142. Cheng, L.-T., Y. Xie, J. Dzubiella, J.A. McCammon, J. Che, B. Li. Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. J. Chem. Theory Comput. 5, 257-266 (2009). [PubMed]
  143. Cheng, Y., M.J. Holst, J.A. McCammon. Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase. In "Biocomputing 2009: Proceedings of the Pacific Symposium," Vol. 14, R.B. Altman, A.K. Dunker, L. Hunter, T. Murray, and T.E. Klein, Eds., World Scientific, pp. 281-292 (2009). [PubMed]
  144. Swift, R.V., J. Durrant, R.E. Amaro, J.A. McCammon. Toward Understanding the Conformational Dynamics of RNA Ligation. Biochemistry 48, 709-719 (2009). [PubMed]
  145. Durrant, J.D., R.E. Amaro, J.A. McCammon. AutoGrow: A Novel Algorithm for Protein Inhibitor Design. Chem. Biol. & Drug Des. 73, 168-178 (2009). [PubMed]
  146. Amaro, R.E., X. Cheng, I. Ivanov, D. Xu, J.A. McCammon. Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-point Free Energy Calculations. J. Amer. Chem. Soc. 131, 4702-4709 (2009). [PubMed]
  147. Wong, S., R.E. Amaro, J.A. McCammon. MM-PBSA captures key role of intercalating water at a protein-protein interface. J. Chem. Theory Comput. 5, 422-429 (2009). [PubMed]
  148. Khavrutskii, I.V., A.A. Gorfe, B. Lu, J.A. McCammon. Free Energy for the Permeation of Na+ and Cl- Ions and their Ion-Pair through Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads. J. Amer. Chem. Soc. 131, 1706-1716 (2009). [PubMed]
  149. Babakhani, A., T.T. Talley, P. Taylor, J.A. McCammon. A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput. Biol. and Chem. 33, 160-170 (2009). [PubMed]
  150. Wang, H.-L., R. Toghraee, D. Papke, X.-L. Cheng, J.A. McCammon, U. Ravaioli, S.M. Sine. Single-channel current through nicotinic receptor produced by closure of binding site C-loop. Biophys. J. 96, 3582-3590 (2009). [PubMed]
  151. Agrawal, A., C.A.F. de Oliveira, Y. Cheng, J.A. Jacobsen, J.A. McCammon, S.M. Cohen. Thioamide Hydroxypyrothiones Supersede Amide Hydroxypyrothiones in Potency Against Anthrax Lethal Factor. J. Med. Chem. 52, 1063-1074 (2009). [PubMed]
  152. Xu, D., E.I. Newhouse, R.E. Amaro, H.C. Pao, L.S. Cheng, P.R.L. Markwick, J.A. McCammon, W.W. Li, P.W. Arzberger. Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective. J. Mol. Biol. 387, 465-491 (2009). [PubMed]
  153. Grant, B.J., A.A. Gorfe, J.A. McCammon. Ras Conformational Switching: Simulating Nucleotide Dependent Conformational Transitions with Accelerated Molecular Dynamics. PLoS Comput. Biol. 5, e1000325 (2009). [PubMed]
  154. Lawrenz, M., R. Baron, J.A. McCammon. Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. J. Chem. Theory Comput. 5, 1106-1116 (2009). [PubMed]
  155. Swift, R.V., J.A. McCammon. Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme. J. Amer. Chem. Soc. 131, 5126-5133 (2009). [PubMed]
  156. Cheng, X., I. Ivanov, H. Wang, S.M. Sine, J.A. McCammon. Molecular Dynamics Simulations of ELIC - a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor. Biophys. J. 96, 4502-4513 (2009). [PubMed]
  157. Fajer, M., R.V. Swift, J.A. McCammon. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J. Comput. Chem. 30, 1719-1725 (2009). [PubMed]
  158. Ivetac, A., J.A. McCammon. Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multi-Copy Molecular Dynamics Simulations. J. Mol. Biol. 388, 644-658 (2009). [PubMed]
  159. McCammon, J.A. Darwinian biophysics: Electrostatics and evolution in the kinetics of molecular binding (Commentary). Proc. Natl. Acad. Sci. USA 106, 7683-7684 (2009). [PubMed]
  160. Knight, J.D.R., D. Hamelberg, J.A. McCammon, R. Kothary. The role of conserved water molecules in the catalytic domain of protein kinases. Proteins: Str. Fn. Bioinf. 76, 527-535 (2009). [PubMed]
  161. Lu, B., X. Cheng, J. Huang, J.A. McCammon. An adaptive fast multipole boundary element method for Poisson-Boltzmann electrostatics. J. Chem. Theory Comput. 5, 1692-1699 (2009). [PubMed]
  162. Burke, J.E., A. Babakhani, A.A. Gorfe, G. Kokotos, S. Li, V.L. Woods, Jr., J.A. McCammon, E.A. Dennis. Location of Inhibitors Bound to Group IVA Phospholipase A2 Determined by Molecular Dynamics and Deuterium Exchange Mass Spectrometry. J. Amer. Chem. Soc. 131, 8083-8091 (2009). [PubMed]
  163. Baron, R., C. Riley, P. Chenprakhon, K. Thotsaporn, R.T. Winter, A. Alfieri, F. Forneris, W.J.H. van Berkel, P. Chaiyen, M.W. Fraaije, A. Mattevi, J.A. McCammon. Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc. Natl. Acad. Sci. USA 106, 10603-10608 (2009). [PubMed]
  164. Gorfe, A.A., B. Lu, Z. Yu, J.A. McCammon. Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer. Biophys. J. 97, 897-905 (2009). [PubMed]
  165. Cervantes, C.F., P.R.L. Markwick, S.-C. Sue, J.A. McCammon, H.J. Dyson, E.A. Komives. Functional Dynamics of the Folded Ankyrin Repeats of I$\kappa\mathrm{B}\alpha$ Revealed by Nuclear Magnetic Resonance. Biochemistry 48, 8023-8031 (2009). [PubMed]
  166. Cheng, L.-T., Z. Wang, P. Setny, J. Dzubiella, B. Li, J.A. McCammon. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J. Chem. Phys. 131, article 144102 (2009). [PubMed]
  167. Baron, R., P.H. Hünenberger, J.A. McCammon. Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: Correction terms and convergence properties. J. Chem. Theory Comput. 5, 3150-3160 (2009). [PubMed]
  168. Newhouse, E.I., D. Xu, P.R.L. Markwick, R.E. Amaro, H.C. Pao, K.J. Wu, M. Alam, J.A. McCammon, W.W. Li. Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective. J. Amer. Chem. Soc. 131, 17430-17442 (2009). [PubMed]
  169. Baron, R., J.A. McCammon, A. Mattevi. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: Structural biology and biomolecular simulation. Curr. Opin. Struct. Biol. 19, 672-679 (2009). [PubMed]
  170. Setny, P., Z. Wang, L.T. Cheng, B. Li, J.A. McCammon, J. Dzubiella. Dewetting-controlled binding of ligands to hydrophobic pockets. Phys. Rev. Letters 103, article 187801 (2009). [PubMed]
  171. Markwick, P.R.L., G. Bouvignies, L. Salmon, J.A. McCammon, M. Nilges, M. Blackledge. Toward a Unified Representation of Protein Structural Dynamics in Solution. J. Amer. Chem. Soc. 131, 16968-16975 (2009). [PubMed]
  172. Khavrutskii, I.V., B. Grant, S.S. Taylor, J.A. McCammon. A transition path ensemble study reveals a linchpin role for Mg2+ during rate-limiting ADP release from protein kinase A. Biochemistry 48, 11532-11545 (2009). [PubMed]

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