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Burger A., Walczak A.M, Wolynes P.G.  2010.  Abduction and asylum in the lives of transcription factors. Proc. Nat. Acad. Sci. USA. 107:4016-4021.
Shen N., Datta D., Schaffer C.B., LeDuc P., Inger D.E., Mazur E..  2005.  Ablation of Cytoskeletal Filaments and Mitochondria in Live Cells using a Femtosecond Laser Nanoscissor. 2:17-25.
Walczak A.M, Onuchic J.N, Wolynes P.G.  2005.  Absolute Rate Theories of Epigenetic Stability. 102:18926-18931.
Baron R., Hunenberger P.H, McCammon J.A.  2009.  Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties. J. Chem. Theor. Comp.. 5:3150-3160.
Minh D.DL, Hamelberg D., McCammon A..  2007.  Accelerated entropy estimates with accelerated dynamics. Journal of Chemical Physics. 127
Hamelberg D., Mongan J., McCammon J.A.  2004.  Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules. Journal of Chemical Physics. 120:11919-11929.
Bucher D., Grant B.J, Markwick P.R, McCammon J.A.  2011.  Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics. Plos Comp. Biol.. 7
Whitford P.C, Geggier P., Altman R.B, Blanchard S.C, Onuchic J.N, Sanbonmatsu K.Y.  2010.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. 16:1196-1204.
Sinko W., Lindert S., McCammon J.A.  2013.  Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design. Chemical Biology & Drug Design. 81:41-49.
Bui J.M, Tai K., McCammon J.A.  2004.  Acetylcholinesterase: Enhanced Fluctuations and Alternative Routes to the Active Site in the Complex with Fasciculin-2. J. Am. Chem. Soc.. 126:7198-7205.
Cheng Y., Cheng X., Radic Z., McCammon J.A.  2007.  Acetylcholinesterase: Mechanisms of Covalent Inhibition of Wild-type and H447I Mutant Determined by Computational Analyses. J. Am. Chem. Soc.. 129:6662-6570.
Bui J.M, McCammon A.J.  2005.  Acetylcholinesterase: Pivotal Roles of its Long Omega Loop (Cys69-Cys96) in Regulating Binding. Chem. Biol. Interact.. 157:357-59.
Hecht I., Skoge M.L, Charest P.G, Ben-Jacob E., Firtel R.A, Loomis W.F, Levine H., Rappel W.J.  2011.  Activated Membrane Patches Guide Chemotactic Cell Motility. Plos Comp. Biol.Plos Computational Biology. 7:12.
Wang S.S, Wolynes P.G.  2012.  Active contractility in actomyosin networks. Proc. Nat. Acad. Sci. USA. 109:6446-6451.
Mehta S.B, Whitmer D., Figueroa R., Williams B.A, Kleinfeld D..  2007.  Active spatial perception in the vibrissa scanning sensorimotor system. Plos Biology. 5:309-322.
Volman V., Levine H..  2008.  Activity-dependent stochastic resonance in recurrent neuronal networks. Physical Review E. 77
Rappel W.J, Firtel R.A.  2012.  Adaptation in a eukaryotic pathway Combining experiments with modeling. Cell Cycle. 11:1051-1052.
Hamacher K..  2006.  Adaptation in stochastic tunneling global optimization of complex potential energy landscapes. 74:944-950.
Lu B.Z, Cheng X.L, Huang J.F, McCammon J.A.  2009.  An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. 5:1692-1699.
Sharpee T.O.  2012.  Adaptive Switches in Midbrain Circuits. Neuron. 73:6-7.
Hou T.J, Wang J.M, Zhang W., Xu X.J.  2007.  ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules? J. Chem. Info. Model.. 47:460-463.
Hou T.J, Wang J.M, Zhang W., Xu X.J.  2007.  ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification. J. Chem. Info. Model.. 47:208-218.
Hou T.J, Wang J.M, Li Y.Y.  2007.  ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine. J. Chem. Info. Model.. 47:2408-2415.
Lu B.Z, Cheng X.L, Huang J.F, McCammon J.A.  2010.  AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. Comp. Phys. Comm.. 181:1150-1160.
Gao F., Bren N., Burghardt T.P, Hansen S., Henchman R.H, Taylor P., McCammon J.A, Sine S.M.  2005.  Agonist-Mediated Conformational Changes in Acetylcholine-Binding Protein Revealed by Simulation and Intrinsic Tryptophan Fluorescence. 280:8443-8451.

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