Miao Y, Nichols SE, McCammon JA (2014)
Mapping of allosteric druggable sites in activation-associated conformers of the m2 muscarinic receptor
Chemical Biology Drug Des 83: 237
Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA (2013)
Simulations of biased agonists in the beta(2) adrenergic receptor with accelerated molecular dynamics
Biochemistry 52: 5593
Cheng Y, Kekenes-Huskey P, Hake J, Holst M, McCammon JA, Michailova A (2012)
Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction
Comput Sci Discov 5:
Lu B, McCammon JA (2010)
Kinetics of diffusion-controlled enzymatic reactions with charged substrates
PMC Biophys 3: 1
Babakhani A, Talley TT, Taylor P, McCammon JA (2009)
A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach
Comput Biol Chem 33: 160
Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA (2009)
Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor
Biophysical Journal 96: 4502
Wang HL, Toghraee R, Papke D, Cheng XL, McCammon JA, Ravaioli U, Sine SM (2009)
Single-channel current through nicotinic receptor produced by closure of binding site C-loop
Biophysical Journal 96: 3582
Cheng YH, Cheng XL, Radic Z, McCammon JA (2008)
Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses
Chemico-Biological Interactions 175: 196
Gorfe AA, Chang CE, Ivanov I, McCammon JA (2008)
Dynamics of the acetylcholinesterase tetramer
Biophysical Journal 94: 1144
Wang HL, Cheng X, Taylor P, McCammon JA, Sine SM (2008)
Control of cation permeation through the nicotinic receptor channel
PLoS Comput Biol 4: e41
Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA (2008)
Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach
J Phys Chem B 112: 270
Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA (2007)
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor
Biophysical Journal 93: 2622
Cheng Y, Cheng X, Radic Z, McCammon JA (2007)
Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses
Journal of the American Chemical Society 129: 6562
Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA (2007)
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations
Biophysical Journal 92: 3397
Ivanov I, Cheng X, Sine SM, McCammon JA (2007)
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family
J Am Chem Soc 129: 8217
Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA (2007)
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution
J Chem Phys 127: 135102
Bui JM, Radic Z, Taylor P, McCammon JA (2006)
Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase
Biophysical Journal 90: 3280
Bui JM, McCammon JA (2006)
Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism
Proc Natl Acad Sci U S A 103: 15451
Cheng X, Wang H, Grant B, Sine SM, McCammon JA (2006)
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors
PLoS Comput Biol 2: e134
Lu B, Cheng X, Huang J, McCammon JA (2006)
Order N algorithm for computation of electrostatic interactions in biomolecular systems
Proc Natl Acad Sci U S A 103: 19314
Senapati S, Cheng Y, McCammon JA (2006)
In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions
Journal of Medicinal Chemistry 49: 6222
Bui JM, McCammon JA (2005)
Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding
Chemico-Biological Interactions 157-158: 357
Gao F, Bren N, Burghardt TP, Hansen S, Henchman RH, Taylor P, McCammon JA, Sine SM (2005)
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence
Journal of Biological Chemistry 280: 8443
Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA (2005)
Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain
Biophysical Journal 88: 2564
Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA (2005)
The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2
Biophysical Journal 89: L25
Senapati S, Bui JM, McCammon JA (2005)
Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a molecular dynamics study
Journal of Medicinal Chemistry 48: 8155
Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA (2005)
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods
Biophysical Journal 88: 1659
Zhang D, McCammon JA (2005)
The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis
PLoS Comput Biol 1: e62
Bui JM, McCammon JA (2004)
The displacement of ligand through the bottleneck region of the acetylcholinesterase gorge
In: Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects (Inestrosa NC, Campos EO) P. Universidad Catolica de Chile-FONDAP Biomedicina: 207
Bui JM, Straatsma T, McCammon JA (2004)
Poster (69) The dynamics of ligand barrier-crossing transitions inside. the acetylcholinesterase gorge
In: Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects (Inestrosa NC, Campos EO) P. Universidad Catolica de Chile-FONDAP Biomedicina: 357
Bui JM, Tai K, McCammon JA (2004)
Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2
Journal of the American Chemical Society 126: 7198
Henchman R, Tai K, Shen T, McCammon JA (2004)
Influence of water on the function of acetylcholinesterase.
Cholinergic Mechanisms, CRC Press
Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA (2004)
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations
Biophysical Journal 86: 2017
Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA (2004)
Mechanism of acetylcholinesterase inhibition by fasciculin.
Cholinergic Mechanisms, CRC Press
Bui JM, Henchman RH, McCammon JA (2003)
The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge
Biophysical Journal 85: 2267
Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA (2003)
Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation
Biophysical Journal 85: 3007
Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA (2003)
Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach
Protein Science 12: 2675
Shi J, Tai K, McCammon JA, Taylor P, Johnson DA (2003)
Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop
Journal of Biological Chemistry 278: 30905
Henchman RH, Tai K, Shen T, McCammon JA (2002)
Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation
Biophysical Journal 82: 2671
Henchman RH, McCammon JA (2002)
Structural and dynamic properties of water around acetylcholinesterase
Protein Science 11: 2080
Kua J, Zhang Y, McCammon JA (2002)
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach
J Am Chem Soc 124: 8260
Shen T, Tai K, Henchman RH, McCammon JA (2002)
Molecular dynamics of acetylcholinesterase
Acc Chem Res 35: 332
Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA (2002)
Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation
Journal of the American Chemical Society 124: 6153
Zhang Y, Kua J, McCammon JA (2002)
Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An ab initio QM/MM Study
J Am Chem Soc 124: 10572
Ondrechen MJ, Briggs JM, McCammon JA (2001)
A model for enzyme-substrate interaction in alanine racemase
J Am Chem Soc 123: 2830
Shen TY, Tai K, McCammon JA (2001)
Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase
Phys Rev E Stat Nonlin Soft Matter Phys 63: 041902
Tai K, Shen T, Borjesson U, Philippopoulos M, McCammon JA (2001)
Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase
Biophysical Journal 81: 715
Wlodek ST, Shen T, McCammon JA (2000)
Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations
Biopolymers 53: 265
Baker NA, Helms V, McCammon JA (1999)
Dynamical properties of fasciculin-2
Proteins 36: 447
Elcock AH, Gabdoulline RR, Wade RC, McCammon JA (1999)
Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin
Journal of Molecular Biology 291: 149
Tara S, Straatsma TP, McCammon JA (1999)
Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations
Biopolymers 50: 35
Tara S, Helms V, Straatsma TP, McCammon JA (1999)
Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A
Biopolymers 50: 347
Baker NA, Huber G, McCammon JA (1998)
Weighted-Ensemble Brownian Dynamics for Charged Ligand Diffusion onto Acetylcholinesterase
In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp.: 367
McCammon JA, Wlodek ST, Clark TW, Kirchhoff P, Scott LR, Tara S (1998)
Computer Simulation Studies of Acetylcholinesterase Dynamics and Activity
In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp.: 327
Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA (1998)
Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge
Biopolymers 46: 465
Wlodek ST, Clark TW, McCammon JA (1998)
Molecular Dynamics of Acetylcholinesterase Dimer
In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp.: 369
Zhou HX, Briggs JM, Tara S, McCammon JA (1998)
Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site
Biopolymers 45: 355
Zhou HX, Wlodek ST, McCammon JA (1998)
Conformation gating as a mechanism for enzyme specificity
Proceedings of the National Academy of Sciences of the United States of America 95: 9280
Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P (1997)
Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin
Journal of Biological Chemistry 272: 23265
Antosiewicz J, Wlodek ST, McCammon JA (1996)
Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site
Biopolymers 39: 85
Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL (1996)
Binding of tacrine and 6-chlorotacrine by acetylcholinesterase
Biopolymers 38: 109
Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK (1995)
Simulation of charge-mutant acetylcholinesterases
Biochemistry 34: 4211
Antosiewicz J, Gilson MK, Lee IH, McCammon JA (1995)
Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand
Biophysical Journal 68: 62
Wlodek ST, Antosiewicz J, Gilson MK, McCammon JA, Clark TW, Scott LR (1995)
Computer Modeling of Acetylcholinesterase and Acetylcholinesterase-Ligand Complexes
In Enzyme of the Cholinesterase Family - Proceedings of Fifth International Meeting on Cholinesterases (Quinn, D.M., Balasubramanian, A.S., Doctor, B.P., Taylor, P., Eds) Plenum Publishing Corp.: 97
Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL (1994)
Open back door in a molecular dynamics simulation of acetylcholinesterase
Science 263: 1276
Tan RC, Truong TN, McCammon JA, Sussman JL (1993)
Acetylcholinesterase: electrostatic steering increases the rate of ligand binding
Biochemistry 32: 401