The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target...
Control of Cation Permeation through the Nicotinic Receptor Channel (2008)
Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J. Andrew McCammon, Steven M. Sine
We used molecular dynamics (MD) simulations to explore the transport of single cations through the channel of the muscle nicotinic acetylcholine receptor (nAChR). Four MD simulations of 16 ns were...
Molecular surface-free continuum model for electrodiffusion processes (2008)
Lu, Benzhuo, McCammon, J. Andrew
Incorporation of van der Waals interactions enables the continuum model of electrodiffusion in biomolecular system to avoid the artifacts of introducing a molecular surface and the painful task of...
Control of cation permeation through the nicotinic receptor channel (2008)
Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J Andrew McCammon, Steven M Sine
We used molecular dynamics (MD) simulations to explore the transport of single cations through the channel of the muscle nicotinic acetylcholine receptor (nAChR). Four MD simulations of 16 ns were...
Lu, Benzhuo, Zhou, Y. C., Huber, Gary A., Bond, Stephen D., Holst, Michael J., McCammon, J. Andrew
A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of...
Lu, Benzhuo, Cheng, Xiaolin, McCammon, J. Andrew
In this paper, we present an efficient and accurate numerical algorithm for calculating the electrostatic interactions in biomolecular systems. In our scheme, a boundary integral equation (BIE)...
Cheng, Xiaolin, Wang, Hailong, Grant, Barry, Sine, Steven M, McCammon, J Andrew
The initial coupling between ligand binding and channel gating in the human alpha 7 nicotinic acetylcholine receptor (nAChR) has been investigated with targeted molecular dynamics (TMD) simulation....
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors (2006)
Xiaolin Cheng, Hailong Wang, Barry Grant, Steven M. Sine, J. Andrew McCammon
The initial coupling between ligand binding and channel gating in the human α7 nicotinic acetylcholine receptor (nAChR) has been investigated with targeted molecular dynamics (TMD) simulation....
Dependency Map of Proteins in the Small Ribosomal Subunit (2006)
Kay Hamacher, Joanna Trylska, J. Andrew McCammon
The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations...
Zhang, Deqiang, McCammon, J Andrew
Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists...
Deqiang Zhang, J. Andrew McCammon
Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists...
Finite Element Solution of the Steady-State Smoluchowski Equation for (2004)
Yuhua Song, Yongjie Zhang, Y Tongye Shen, Z Ch, Rajit L. Bajaj, J. Andrew Mccammon, ...
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been...
Electrostatics of Nanosystems: (2004)
Nathan A. Baker, David Sept, Simpson Joseph, Michael J. Holst, J. Andrew Mccammon
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the...
Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions (2003)
Kaihsu Tai, Stephen D. Bond, Hugh R. Macmillan, Nathan Andrew Baker, Michael Jay Holst, J. Andrew Mccammon, ...
A robust infrastructure for solving time-dependent diffusion using the finite element package FEtk has been developed to simulate synaptic transmission in a neuromuscular junction with realistic...
Electrostatic Steering of Substrate to Acetylcholinesterase: Analysis of Field Fluctuations (2001)
Stanislaw T. Wlodek, Tongye Shen, J. Andrew Mccammon
Based on previous molecular dynamics simulation results for acetylcholinesterase dimer, we calculate and analyse the electrostatic field fluctuations around the enzyme. The results show that dynamic...
Willy Wriggers, Ronald A. Milligan, J. Andrew Mccammon
INTRODUCTION The role of visualization in structural biology is currently expanding, as novel modeling and graphics tools begin to integrate data from a variety of biophysical sources (Bajaj, 1998)....
Parallelizing Molecular Dynamics using Spatial Decomposition (1999)
Reinhard V. Hanxleden, Terry W. Clark, Reinhard Hanxleden, J. Andrew Mccammon, L. Ridgway Scott
Several algorithms have been used for parallel molecular dynamics, including the replicated algorithm and those based on spatial decompositions. The replicated algorithm stores the entire system's...
Molecular Dynamics of Acetylcholinesterase Dimer complexed with Tacrine. (1999)
Stanislaw T. Wlodek, Terry W. Clark, L. Ridgway Scott, J. Andrew Mccammon
We have studied the dynamic properties of acetylcholinesterase dimer from Torpedo californica liganded with tacrine (AChE-THA) in solution using molecular dynamics. The simulation reveals...
I/O Limitations in Parallel Molecular Dynamics (1999)
Terry W. Clark, L. Ridgway Scott, Stanislaw Wlodek, J. Andrew Mccammon
We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production can be overwhelming, exceeding...
J. Andrew Mccammon, Christopher Darrell Rosin
: : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : xii I Introduction : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 1 A. Adversarial Problems : : : : : : :...
Self-organizing Neural Networks Bridge the Biomolecular Resolution Gap (1998)
Willy Wriggers, Ronald A. Milligan, Klaus Schulten, J. Andrew Mccammon
y and medicine depend on an understanding of fundamental cellular processes, most of which involve the actions and interactions of large biomolecular aggregates. Three-dimensional (3D) image...
Parallelizing Molecular Dynamics using Spatial Decomposition (1997)
Reinhard V. Hanxleden, Terry W. Clark, Reinhard Hanxleden, J. Andrew Mccammon, L. Ridgway Scott
Several algorithms have been used for parallel molecular dynamics, including the replicated algorithm and those based on spatial decompositions. The replicated algorithm stores the entire system's...
I/O Limitations in Parallel Molecular Dynamics (1995)
Terry W. Clark, L. Ridgway Scott, Stanislaw Wlodek, J. Andrew Mccammon
We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production can be overwhelming, exceeding...
I/O Limitations in Parallel Molecular Dynamics (1995)
Terry W. Clark, L. Ridgway Scott, Stanislaw Wlodek, J. Andrew Mccammon
We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production can be overwhelming, exceeding...
Ordinary Differential Equations of Molecular Dynamics (1995)
J. Andrew Mccammon, B. Montgomery Pettitt, L. Ridgway Scott
The ordinary differential equations of Newtonian dynamics are used in atomic simulations with the method of molecular dynamics. The basic issues are surveyed and standard algorithms are described....
Parallelizing Molecular Dynamics using Spatial Decomposition (1994)
Reinhard V. Hanxleden, Terry W. Clark, Reinhard Hanxleden, J. Andrew Mccammon, L. Ridgway Scott
Several algorithms have been used for parallel molecular dynamics, including the replicated algorithm and those based on spatial decompositions. The replicated algorithm stores the entire system's...
Parallelization Strategies for a Molecular Dynamics Program (1992)
Terry W. Clark, Reinhard V. Hanxleden, J. Andrew Mccammon, L. Ridgway Scott
A molecular-dynamics program typically takes several man-years to write and therefore is representative for a large class of scientific programs whose rewriting should not be taken lightly. This...
Dynamics of proteins and nucleic acids / J. Andrew McCammonStephen C. Harvey (1987)
McCammon, J. Andrew, Harvey, Stephen C
Incluye bibliografía e índice
Parallel Molecular Dynamics (1970)
Terry W. Clark, J. Andrew Mccammon, L. Ridgway Scott
. We describe the results of a preliminary port of a large molecular dynamics (MD) code, gromos [15], to a distributed--memory parallel computer. The objectives of this study were three fold. First,...
Conformation gating as a mechanism for enzyme specificity
Zhou, Huan-Xiang, Wlodek, Stanislaw T., McCammon, J. Andrew
Acetylcholinesterase, with an active site located at the bottom of a narrow and deep gorge, provides a striking example of enzymes with buried active sites. Recent molecular dynamics simulations...
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins
Weber, Wolfgang, Helms, Volkhard, McCammon, J. Andrew, Langhoff, Peter W.
Recent experiments on various similar green fluorescent protein (GFP) mutants at the single-molecule level and in solution provide evidence of previously unknown short- and long-lived “dark”...
Identification of protein oligomerization states by analysis of interface conservation
Elcock, Adrian H., McCammon, J. Andrew
The discrimination of true oligomeric protein–protein contacts from nonspecific crystal contacts remains problematic. Criteria that have been used previously base the assignment of oligomeric state...
Electrostatics of nanosystems: Application to microtubules and the ribosome
Baker, Nathan A., Sept, David, Joseph, Simpson, Holst, Michael J., McCammon, J. Andrew
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the...
Quantum simulation of nuclear rearrangement in electron transfer reactions
Zheng, Chong, McCammon, J. Andrew, Wolynes, Peter G.
A quantum simulation scheme based on the path integral molecular dynamics technique has been used to calculate the effective activation energies associated with nuclear rearrangement in the electron...
PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
Dolinsky, Todd J., Nielsen, Jens E., McCammon, J. Andrew, Baker, Nathan A.
Continuum solvation models, such as Poisson–Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular...
A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor
Law, Richard J., Henchman, Richard H., McCammon, J. Andrew
The nicotinic acetylcholine receptor is a well characterized ligandgated ion channel, yet a proper description of the mechanisms involved in gating, opening, closing, ligand binding, and...
Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies
Resat, Haluk, Marrone, Tami J., McCammon, J. Andrew
Studying the thermodynamics of biochemical association reactions at the microscopic level requires efficient sampling of the configurations of the reactants and solvent as a function of the reaction...
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis
Zhang, Deqiang, McCammon, J. Andrew
Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists...
Henchman, Richard H, Tai, Kaihsu, Shen, Tongye, McCammon, J Andrew
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may...
Bridging implicit and explicit solvent approaches for membrane electrostatics.
Lin, Jung-Hsin, Baker, Nathan A, McCammon, J Andrew
Conformations of a zwitterionic bilayer were sampled from a molecular dynamics simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit...
Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions
Tai, Kaihsu, Bond, Stephen D., MacMillan, Hugh R., Baker, Nathan Andrew, Holst, Michael Jay, McCammon, J. Andrew
A robust infrastructure for solving time-dependent diffusion using the finite element package FEtk has been developed to simulate synaptic transmission in a neuromuscular junction with realistic...
The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase Gorge
Bui, Jennifer M., Henchman, Richard H., McCammon, J. Andrew
The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of...
Henchman, Richard H., Wang, Hai-Long, Sine, Steven M., Taylor, Palmer, McCammon, J. Andrew
A homology model of the ligand binding domain of the α7 nicotinic receptor is constructed based on the acetylcholine-binding protein crystal structure. This structure is refined in a 10 ns molecular...
Swanson, Jessica M. J., Henchman, Richard H., McCammon, J. Andrew
The prediction of absolute ligand-receptor binding affinities is essential in a wide range of biophysical queries, from the study of protein-protein interactions to structure-based drug design....
Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan A.
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been...
Zhang, Deqiang, Suen, Jason, Zhang, Yongjie, Song, Yuhua, Radic, Zoran, Taylor, Palmer, ...
The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of...
Dependency Map of Proteins in the Small Ribosomal Subunit
Hamacher, Kay, Trylska, Joanna, McCammon, J. Andrew
The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations...
Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain
Henchman, Richard H., Wang, Hai-Long, Sine, Steven M., Taylor, Palmer, McCammon, J. Andrew
Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states....
Exploring Global Motions and Correlations in the Ribosome
Trylska, Joanna, Tozzini, Valentina, McCammon, J. Andrew
We studied slower global coupled motions of the ribosome with half a microsecond of coarse-grained molecular dynamics. A low-resolution anharmonic network model that allows for the evolution of...
Minh, David D. L., Bui, Jennifer M., Chang, Chia-en, Jain, Tushar, Swanson, Jessica M. J., McCammon, J. Andrew
Protein-protein association is accompanied by a large reduction in translational and rotational (external) entropy. Based on a 15 ns molecular dynamics simulation of acetylcholinesterase (AChE) in...
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors
Cheng, Xiaolin, Wang, Hailong, Grant, Barry, Sine, Steven M, McCammon, J. Andrew
The initial coupling between ligand binding and channel gating in the human α7 nicotinic acetylcholine receptor (nAChR) has been investigated with targeted molecular dynamics (TMD) simulation....
Conformation gating as a mechanism for enzyme specificity
Zhou, Huan-Xiang, Wlodek, Stanislaw T., McCammon, J. Andrew
Acetylcholinesterase, with an active site located at the bottom of a narrow and deep gorge, provides a striking example of enzymes with buried active sites. Recent molecular dynamics simulations...
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins
Weber, Wolfgang, Helms, Volkhard, McCammon, J. Andrew, Langhoff, Peter W.
Recent experiments on various similar green fluorescent protein (GFP) mutants at the single-molecule level and in solution provide evidence of previously unknown short- and long-lived “dark”...
Identification of protein oligomerization states by analysis of interface conservation
Elcock, Adrian H., McCammon, J. Andrew
The discrimination of true oligomeric protein–protein contacts from nonspecific crystal contacts remains problematic. Criteria that have been used previously base the assignment of oligomeric state...
Electrostatics of nanosystems: Application to microtubules and the ribosome
Baker, Nathan A., Sept, David, Joseph, Simpson, Holst, Michael J., McCammon, J. Andrew
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the...
Quantum simulation of nuclear rearrangement in electron transfer reactions
Zheng, Chong, McCammon, J. Andrew, Wolynes, Peter G.
A quantum simulation scheme based on the path integral molecular dynamics technique has been used to calculate the effective activation energies associated with nuclear rearrangement in the electron...
PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
Dolinsky, Todd J., Nielsen, Jens E., McCammon, J. Andrew, Baker, Nathan A.
Continuum solvation models, such as Poisson–Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular...
A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor
Law, Richard J., Henchman, Richard H., McCammon, J. Andrew
The nicotinic acetylcholine receptor is a well characterized ligandgated ion channel, yet a proper description of the mechanisms involved in gating, opening, closing, ligand binding, and...
Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies
Resat, Haluk, Marrone, Tami J., McCammon, J. Andrew
Studying the thermodynamics of biochemical association reactions at the microscopic level requires efficient sampling of the configurations of the reactants and solvent as a function of the reaction...
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis
Zhang, Deqiang, McCammon, J. Andrew
Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists...
Henchman, Richard H, Tai, Kaihsu, Shen, Tongye, McCammon, J Andrew
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may...
Bridging implicit and explicit solvent approaches for membrane electrostatics.
Lin, Jung-Hsin, Baker, Nathan A, McCammon, J Andrew
Conformations of a zwitterionic bilayer were sampled from a molecular dynamics simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit...
Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions
Tai, Kaihsu, Bond, Stephen D., MacMillan, Hugh R., Baker, Nathan Andrew, Holst, Michael Jay, McCammon, J. Andrew
A robust infrastructure for solving time-dependent diffusion using the finite element package FEtk has been developed to simulate synaptic transmission in a neuromuscular junction with realistic...
The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase Gorge
Bui, Jennifer M., Henchman, Richard H., McCammon, J. Andrew
The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of...
Henchman, Richard H., Wang, Hai-Long, Sine, Steven M., Taylor, Palmer, McCammon, J. Andrew
A homology model of the ligand binding domain of the α7 nicotinic receptor is constructed based on the acetylcholine-binding protein crystal structure. This structure is refined in a 10 ns molecular...
Swanson, Jessica M. J., Henchman, Richard H., McCammon, J. Andrew
The prediction of absolute ligand-receptor binding affinities is essential in a wide range of biophysical queries, from the study of protein-protein interactions to structure-based drug design....
Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan A.
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been...
Zhang, Deqiang, Suen, Jason, Zhang, Yongjie, Song, Yuhua, Radic, Zoran, Taylor, Palmer, ...
The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of...
Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain
Henchman, Richard H., Wang, Hai-Long, Sine, Steven M., Taylor, Palmer, McCammon, J. Andrew
Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states....
Dependency Map of Proteins in the Small Ribosomal Subunit
Hamacher, Kay, Trylska, Joanna, McCammon, J. Andrew
The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations...