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, pp. 41-46 (2005). [PDF]
  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., 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. 3, 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 Journal 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. 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.-E. 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 Comp. 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, 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., 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 Comp. 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. DeGrado, J.A. McCammon, M. Klien. Characterization of Non-biological 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.Q., 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. Huebsch, 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).
  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 Comp. 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, 1579-2006 (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. Chem. Med. Chem. 1, 694-697 (2006). [PubMed]
  57. Jain, T.S., D. 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 Comp. 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., 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. 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 Research 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.-E. 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., J. Wagoner, N. 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. Case, A. Onufriev. Generalized Born model with a simple, robust molecular volume correction. J. Chem. Theory Comput. 3, 156-169 (2007).
  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).
  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.-E., 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.-E. 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 molecular dynamics 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. 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. Design 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, 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. Comp. 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 Neglected Tropical Diseases 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. 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).
  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.-E.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).
  107. Amaro, R.E., R. Baron, J.A. McCammon. An Improved Relaxed Complex Scheme for Receptor Flexibility in Computer-Aided Drug Design. J. Comp.-Aid. Molec. Des., in press (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. Chen, P. Taylor, J.A. McCammon, S.M. Sine. Control of cation permeation through the nicotinic receptor channel. PloS Computational Biology 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. Plowan, 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 Journal 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. Lu, S., A. Michailova, J. Saucerman, Y. Cheng, Z. Yu, T. Kaiser, W. Li, R.E. Bank, M. 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., in review (2008).
  116. 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, in press (2008, November).
  117. 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]
  118. 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]
  119. 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, pp. 403-412 (2008).
  120. Gorfe, A.A., B.J. Grant, J.A. McCammon. Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins. Structure, in press (2008).

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