Publications 2010 - 2014

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  1. Durrant, J.D., C.A.F. de Oliveira, J.A. McCammon. Including Receptor Flexibility and Induced Fit Effects into the Design of MMP2 Inhibitors. J. Mol. Recognition 23, 173-182 (2010). [PubMed]
  2. Qin, S., D.D.L. Minh, J.A. McCammon, H.-X. Zhou. Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease. J. Phys. Chem. Letters 1, 107-110 (2010). [PubMed]
  3. Zhou, H.-X., J.A. McCammon. The gates of ion channels and enzymes. Trends Biochem. Sci. 35, 179-185 (2010). [PubMed]
  4. Sivendran, S., V. Jones, D. Sun, Y. Wang, A.E. Grzegorzewicz, M.S. Scherman, A.D. Napper, J.A. McCammon, R.E. Lee, S.L. Diamond, M. McNeil. Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-D-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC). Bioorg. Med. Chem. 18, 896-908 (2010). [PubMed]
  5. Li, B., B. Lu, Z. Wang, J.A. McCammon. Solutions to a Reduced Poisson-Nernst-Planck System and Determination of Reaction Rates. Physica A 389, 1329-1345 (2010). [PubMed]
  6. Durrant, J.D., R.E. Amaro, L. Xie, M.D. Urbaniak, M.A.J. Ferguson, A. Haapalainen, Z. Chen, A.M. Di Guilmi, F. Wunder, P.E. Bourne, J.A. McCammon. A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6, e1000648 (2010). [PubMed]
  7. Markwick, P.R.L., C.F. Cervantes, B.L. Abel, E.A. Komives, M. Blackledge, J.A. McCammon. Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins. J. Amer. Chem. Soc. 132, 1220-1221 (2010). [PubMed]
  8. Grant, B.J., A.A. Gorfe, J.A. McCammon. Large conformational changes in proteins: signaling and other functions. Curr. Opin. Struct. Biol. 20, 142-147 (2010). [PubMed]
  9. Williams, S.L., C.A.F. de Oliveira, J.A. McCammon. Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics. J. Chem. Theory Comput. 6, 560-568 (2010). [PubMed]
  10. Lu, B., J.A. McCammon. Kinetics of diffusion-controlled enzymatic reactions with charged substrates. PMC Biophysics 3, article 1 (2010). [PubMed]
  11. Perryman, A.L., S. Forli, G.M. Morris, C. Burt, Y. Cheng, M.J. Palmer, K. Whitby, J.A. McCammon, C. Phillips, A.J. Olson. A Dynamic Model of HIV Integrase Inhibition and Drug Resistance. J. Mol. Biol. 397, 600-615 (2010). [PubMed]
  12. Sung, J.C., A.W. Van Wynsberghe, R.E. Amaro, W.W. Li, J.A. McCammon. The role of secondary sialic acid binding sites in influenza N1 neuraminidase. J. Amer. Chem. Soc. 132, 2883-2885 (2010). [PubMed]
  13. Lu, B., X. Cheng, J. Huang, J.A. McCammon. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Comput. Phys. Commun. 181, 1150-1160 (2010). [PubMed]
  14. Tainer, J.A., J.A. McCammon, I. Ivanov. Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading. J. Amer. Chem. Soc. 132, 7372-7378 (2010). [PubMed]
  15. Durrant, J.D., H. Keränen, B.A. Wilson, J.A. McCammon. Computational Identification of Uncharacterized Cruzain Binding Sites. PLoS Negl. Trop. Dis. 4, e676 (2010). [PubMed]
  16. Durrant, J.D., J.A. McCammon. Potential Drug-Like Inhibitors of Group 1 Influenza Neuraminidase Identified through Computer-Aided Drug Design. Comput. Biol. and Chem. 34, 97-105 (2010). [PubMed]
  17. Sierecki, E., W. Sinko, J.A. McCammon, A.C. Newton. Discovery of Small Molecule Inhibitors of the PH Domain Leucine-Rich Repeat Protein Phosphatase (PHLPP) by Chemical and Virtual Screening. J. Med. Chem. 53, 6899-6911 (2010). [PubMed]
  18. Peng, L.X., A. Ivetac, A.S. Chaudhari, S. Van, G. Zhao, L. Yu, S.B. Howell, J.A. McCammon, D.A. Gough. Characterization of a clinical polymer-drug conjugate using multiscale modeling. Biopolymers 93, 936-951 (2010). [PubMed]
  19. Bauler, P., G. Huber, T. Leyh, J.A. McCammon. Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics. J. Phys. Chem. Letters 1, 1332-1335 (2010). [PubMed]
  20. Lawrenz, M., J. Wereszczynski, R. Amaro, R. Walker, A. Roitberg, J.A. McCammon. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins 78, 2523-2532 (2010). [PubMed]
  21. Durrant, J.D., M.D. Urbaniak, M.A.J. Ferguson, J.A. McCammon. Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4'-Epimerase Inhibitors: Towards the Development of Novel Therapies for African Sleeping Sickness. J. Med. Chem. 53, 5025-5032 (2010). [PubMed]
  22. Rouffet, M., C.A.F. de Oliveira, Y. Udi, A. Agrawal, I. Sagi, J.A. McCammon, S.M. Cohen. From Sensors to Silencers: Quinoline- and Benzimidazole-Sulfonamides as Inhibitors for Zinc Proteinases. J. Amer. Chem. Soc. 132, 8232-8233 (2010). [PubMed]
  23. Lu, B., M.J. Holst, J.A. McCammon, Y.C. Zhou. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J. Comput. Phys. 229, 6979-6994 (2010). [PubMed]
  24. Ivetac, A., J.A. McCammon. Mapping the druggable allosteric space of G-protein coupled receptors: A fragment-based molecular dynamics approach. Chem. Biol. & Drug Des. 76, 201-217 (2010). [PubMed]
  25. Ishizuka, R., G.A. Huber, J.A. McCammon. Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach. J. Phys. Chem. Letters 1, 2279-2283 (2010). [PubMed]
  26. Huber, G.A., J.A. McCammon. Browndye: A Software Package for Brownian Dynamics. Comput. Phys. Commun. 181, 1896-1905 (2010). [PubMed]
  27. Baron, R., P. Setny, J.A. McCammon. Water in cavity-ligand recognition. J. Amer. Chem. Soc. 132, 12091-12097 (2010). [PubMed]
  28. Setny, P., R. Baron, J.A. McCammon. How can hydrophobic association be enthalpy-driven? J. Chem. Theory Comput. 6, 2866-2871 (2010). [PubMed]
  29. Lukman, S., B.J. Grant, A.A. Gorfe, G.H. Grant, J.A. McCammon. The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput. Biol. 6, e1000922 (2010). [PubMed]
  30. Cheng, Y., Z. Yu, M. Hoshijima, M.J. Holst, A.D. McCulloch, J.A. McCammon, A.P. Michailova. Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput. Biol. 6, e1000972 (2010). [PubMed]
  31. Wereszczynski, J., J.A. McCammon. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. J. Chem. Theory Comput. 6, 3285-3292 (2010). [PubMed]
  32. Durrant, J.D., J.A. McCammon. NNScore: A Neural Network Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Inform. Model. 50, 1865-1871 (2010). [PubMed]
  33. Durrant, J.D., J.A. McCammon. Computer-aided Drug Discovery Techniques that Account for Receptor Flexibility. Curr. Opin. Pharm. 10, 770-774 (2010). [PubMed]
  34. Grant, B.J., J.A. McCammon, A.A. Gorfe. Conformational selection in G-proteins: Lessons from Ras and Rho. Biophys. J. 99, 87-89 (2010). [PubMed]
  35. Durrant, J.D., C.A.F. de Oliveira, J.A. McCammon. POVME: An Algorithm for Measuring Binding-Pocket Volumes. J. Mol. Graph. Model. 29, 773-776 (2011). [PubMed]
  36. Radford, R.J., M. Lawrenz, P.C. Nguyen, J.A. McCammon, F.A. Tezcan. Porous Protein Frameworks with Unsaturated Metal Centers in Sterically Encumbered Coordination Sites. Chem. Commun. 47, 313-315 (2011). [PubMed]
  37. Williams, S.L., C.A.F.D. Oliveira, H. Vazquez, J.A. McCammon. From Zn to Mn: The Study of Novel Manganese-Binding Groups in the Search for New Drugs against Tuberculosis. Chem. Biol. & Drug Des. 77, 117-123 (2011). [PubMed]
  38. Skjaerven, L., B. Grant, A. Muga, K. Teigen, J.A. McCammon, N. Reuter, A. Martinez. Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. PLoS Comput. Biol. 7, e1002004 (2011). [PubMed]
  39. Sander, T., B. Frølund, A.T. Bruun, I. Ivanov, J.A. McCammon, T. Balle. New insights into the GABA(A) receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data. Proteins 79, 1458-1477 (2011). [PubMed]
  40. Thompson, E.E., S.S. Taylor, J.A. McCammon. Protein Kinases: Phosphorylation Machines. In "Molecular Machines," B. Roux, Ed., World Scientific, Ch. 7, pp. 115-130 (2011).
  41. Sinko, W., C. de Oliveira, S. Williams, A. Van Wynsberghe, J.D. Durrant, R. Cao, E. Oldfield, J.A. McCammon. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial. Chem. Biol. & Drug Des. 77, 412-420 (2011). [PubMed]
  42. Ivetac, A., J.A. McCammon. Molecular Recognition in the Case of Flexible Targets. Curr. Pharm. Des. 17, 1663-1671 (2011). [PubMed]
  43. Baron, R., C. Binda, M. Tortorici, J.A. McCammon, A. Mattevi. Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase LSD1-CoREST Complex. Structure 19, 212-220 (2011). [PubMed]
  44. Durrant, J.D., J.A. McCammon. BINANA: A Novel Algorithm for Ligand-Binding Characterization. J. Mol. Graph. Model. 29, 888-893 (2011). [PubMed]
  45. Wang, Y., C.B. Harrison, K. Schulten, J.A. McCammon. Implementation of Accelerated Molecular Dynamics in NAMD. Comput. Sci. & Discovery 4, article 015002 (2011). [PubMed]
  46. McCammon, J.A. Gated Diffusion-controlled Reactions. BMC Biophysics 4, article 4 (2011). [PubMed]
  47. Markwick, P.R.L., L.C.T. Pierce, D.B. Goodin, J.A. McCammon. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. J. Phys. Chem. Letters 2, 158-164 (2011). [PubMed]
  48. Mereghetti, P., D. Kokh, J.A. McCammon, R.C. Wade. Diffusion and Association Processes in Biological Systems: Theory, Computation and Experiments. BMC Biophysics 4, article 2 (2011). [PubMed]
  49. Długosz, M., G.A. Huber, J.A. McCammon, J. Trylska. Brownian dynamics study of the association between the 70S ribosome and the elongation factor G. Biopolymers 95, 616-627 (2011). [PubMed]
  50. Bucher, D., B.J. Grant, P.R. Markwick, J.A. McCammon. Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics Simulations. PLoS Comput. Biol. 7, e1002034 (2011). [PubMed]
  51. Pierce, L.C.T., P.R.L. Markwick, J.A. McCammon, N.L. Doltsinis. Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. J. Chem. Phys. 134, article 174107 (2011). [PubMed]
  52. Bucher, D., L.C.T. Pierce, J.A. McCammon, P.R.L. Markwick. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations. J. Chem. Theory Comput. 7, 890-897 (2011). [PubMed]
  53. Nichols, S.E., R. Baron, A.D. Ivetac, J.A. McCammon. Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. J. Chem. Inform. Model. 51, 1439-1446 (2011). [PubMed]
  54. Romanowska, J., J.A. McCammon, J. Trylska. Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. PLoS Comput. Biol. 7, e1002099 (2011). [PubMed]
  55. Durrant, J.D., C.A.F. de Oliveira, J.A. McCammon. Pyrone-Based Inhibitors of Metalloproteinases Types 2 and 3 May Work as Conformation-Selective Inhibitors. Chem. Biol. & Drug Des. 78, 191-198 (2011). [PubMed]
  56. Wade, R.C., P. Mereghetti, J.A. McCammon (Eds.). Biological Diffusion and Brownian Dynamics. Special thematic series inaugurating volume 4 of BMC Biophysics (2011).
  57. Lawrenz, M., R. Baron, Y. Wang, J.A. McCammon. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J. Chem. Theory Comput. 7, 2224-2232 (2011). [PubMed]
  58. Bucher, D., B.J. Grant, J.A. McCammon. Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein. Biochemistry 50, 10530-10539 (2011). [PubMed]
  59. Williams, S.L., P.G. Blachly, J.A. McCammon. Measuring the Successes and Deficiencies of Constant pH Molecular Dynamics: A Blind Prediction Study. Proteins 79, 3381-3388 (2011). [PubMed]
  60. de Oliveira, C.A.F., B.J. Grant, M. Zhou, J.A. McCammon. Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. PLoS Comput. Biol. 7, e1002178 (2011). [PubMed]
  61. Durrant, J.D., R. Cao, A.A. Gorfe, W. Zhu, J. Li, A. Sankovsky, E. Oldfield, J.A. McCammon. Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design. Chem. Biol. & Drug Des. 78, 323-332 (2011). [PubMed]
  62. Durrant, J.D., J.A. McCammon. HBonanza: A Computer Program for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis. J. Mol. Graph. Model. 31, 5-9 (2011). [PubMed]
  63. Markwick, P.R.L., J.A. McCammon. Studying Functional Dynamics in Bio-molecules using Accelerated Molecular Dynamics. Phys. Chem. Chem. Phys. 13, 20053-20065 (2011). [PubMed]
  64. Wang, Y., P.R.L. Markwick, C.A.F. de Oliveira, J.A. McCammon. Enhanced lipid diffusion and mixing in accelerated molecular dynamics. J. Chem. Theory Comput. 7, 3199-3207 (2011). [PubMed]
  65. Grant, B.J., S. Lukman, H.J. Hocker, J. Sayyah, J.H. Brown, J.A. McCammon, A.A. Gorfe. Novel Allosteric Sites on Ras for Lead Generation. PLoS ONE 6, e25711 (2011). [PubMed]
  66. Wang, Y., T.N. Hess, V. Jones, J.Z. Zhou, M.R. McNeil, J.A. McCammon. Novel Inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose Reductase (RmlD) Identified by Virtual Screening. Bioorg. Med. Chem. Letters 21, 7064-7067 (2011).
  67. Durrant, J.D., J.A. McCammon. Towards the Development of Novel Trypanosoma brucei RNA Editing Ligase 1 Inhibitors. BMC Pharm. 11, article 9 (2011). [PubMed]
  68. Durrant, J.D., A.J. Friedman, J.A. McCammon. CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Inform. Model. 51, 2573-2580 (2011). [PubMed]
  69. Durrant, J.D., J.A. McCammon. Molecular Dynamics Simulations and Drug Discovery. BMC Biol. 9, article 71 (2011). [PubMed]
  70. Grant, B.J., D.M. Gheorghe, W. Zheng, M. Alonso, G. Huber, M. Dlugosz, J.A. McCammon, R.A. Cross. Electrostatically Biased Binding of Kinesin to Microtubules. PLoS Biol. 9, e1001207 (2011). [PubMed]
  71. Durrant, J.D., J.A. McCammon. NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inform. Model. 51, 2897-2903 (2011). [PubMed]
  72. Wereszczynski, J., J.A. McCammon. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Quarterly Revs. of Biophysics, in press (2012). [PubMed]
  73. Holst, M., J.A. McCammon, Z. Yu, Y.C. Zhou, Y. Zhu. Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation. Commun. Comput. Phys. 11, 179-214 (2012). [PubMed]
  74. Wang, Y., J.A. McCammon. Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling. In "Computational Modeling of Biological Systems: From Molecules to Pathways," N.V. Dokholyan, Ed., Springer-Verlag, Ch. 1, in press (2012).
  75. Lawrenz, M., R. Baron, Y. Wang, J.A. McCammon. Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing. In "Computational Drug Discovery and Design," R. Baron, Ed., Springer Series in Methods in Molecular Biology. Humana Press, USA, pp. 469-486 (2012). [PubMed]
  76. Sinko, W., E. Sierecki, C.A.F. de Oliveira, J.A. McCammon. Guide to Virtual Screening: Application to the Akt Phosphatase PHLPP. In "Computational Drug Discovery and Design," R. Baron, Ed., Springer Series in Methods in Molecular Biology. Humana Press, USA, pp. 561-573 (2012). [PubMed]
  77. Ivetac, A., J.A. McCammon. A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites. In "Computational Drug Discovery and Design," R. Baron, Ed., Springer Series in Methods in Molecular Biology, Humana Press, USA, pp. 3-12 (2012). [PubMed]
  78. Wereszczynski, J., J.A. McCammon. Accelerated Molecular Dynamics in Computational Drug Design. In "Computational Drug Discovery and Design," R. Baron, Ed., Springer Series in Methods in Molecular Biology, Humana Press, USA, pp. 515-524 (2012). [PubMed]
  79. Nichols, S.E., R. Baron, J.A. McCammon. On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening. In "Computational Drug Discovery and Design," R. Baron, Ed., Springer Series in Methods in Molecular Biology, Humana Press, USA, pp. 93-103 (2012). [PubMed]
  80. Baron, R., P. Setny, J.A. McCammon. Hydrophobic Association and Volume-confined Water Molecules. In "Protein-ligand Interactions," Vol. ?, H. Gohlke, Ed., Methods and Principles in Medicinal Chemistry Series, Wiley-VCH Publishers (2012).
  81. Zhang, B., B.Z. Lu, X. Cheng, X. Sun, N. Pitsianis, J. Huang, J.A. McCammon. Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver. Commun. Comput. Phys., in press (2012).
  82. Sinko, W., C.A.F. de Oliveira, L.C.T. Pierce, J.A. McCammon. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J. Chem. Theory Comput., in press (2012). [PubMed]
  83. McCammon, J.A. Computer-aided Drug Discovery: Two Antiviral Drugs for HIV/AIDS. In "Innovations in Biomolecular Modelling and Simulations," Vol. 2, Tamar Schlick, Ed., Royal Society of Chemistry, in press (2012).
  84. Wang, Z., J. Che, L.-T. Cheng, J. Dzubiella, B. Li, J.A. McCammon. Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. J. Chem. Theory Comput., in press (2012).
  85. Durrant, J.D., J.A. McCammon. AutoClickChem: Click Chemistry in Silico. PLoS Comput. Biol., in press (2012).
  86. Wang, Y., J.A. McCammon. Accelerated Molecular Dynamics: Theory, Implementation and Application. In "Proceedings of the 2012 Conference on Theory and Applications of Computational Chemistry," E. Clementi, Ed., American Institute of Physics, in press (2012).
  87. Wereszczynski, J., J.A. McCammon. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates. Protein Sci., in press (2012). [PubMed]
  88. Cheng, Y., P. Kekenes-Huskey, J. Hake, M.J. Holst, J.A. McCammon, A.P. Michailova. Multiscale Continuum Modeling and Simulation of Biological Processes: From Molecular Electro-diffusion to Sub-Cellular Signaling Transduction. Comput. Sci. & Discovery, in press (2012).
  89. Lawrenz, M., J. Wereszczynski, J.M. Ortiz-S\'anchez, S.E. Nichols, J.A. McCammon. Thermodynamic integration to predict host-guest binding affinities. J. Comput.-Aided Mol. Des., in press (2012).

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