James Andrew McCammon

Publication Activity (10 Years)

Years Active: 1982-2024
Publications (10 Years): 13

Top Topics

Molecular Dynamics

Protein Folding

Mesh Generation

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, James Andrew McCammon
Oxidase. J. Chem. Inf. Model. 64 (13) (2024)
Terra Sztain, Rommie E. Amaro, James Andrew McCammon
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J. Chem. Inf. Model. 61 (7) (2021)
Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. 16 (4) (2020)
Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. ACM Trans. Math. Softw. 45 (3) (2019)
Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, James Andrew McCammon, Ross C. Walker
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J. Comput. Chem. 39 (19) (2018)
Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael Holst
The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. CoRR (2018)
W. Guan, Xiao-Chun Cheng, J. Huang, G. Huber, Wei Li, James Andrew McCammon, Bo Zhang
RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations. Comput. Phys. Commun. 227 (2018)
Fuhui Fang, Jingfang Huang, Gary A. Huber, James Andrew McCammon, Bo Zhang
Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations. SIAM J. Sci. Comput. 40 (3) (2018)
W. Guan, Xiao-Chun Cheng, J. Huang, G. Huber, Wei Li, James Andrew McCammon, Bo Zhang
RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. CoRR (2017)
Shenggao Zhou, Li-Tien Cheng, Hui Sun, Jianwei Che, Joachim Dzubiella, Bo Li, James Andrew McCammon
LS-VISM: A software package for analysis of biomolecular solvation. J. Comput. Chem. 36 (14) (2015)
Steffen Lindert, Lorillee Tallorin, Quynh G. Nguyen, Michael D. Burkart, James Andrew McCammon
In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J. Comput. Aided Mol. Des. 29 (1) (2015)
Meekyum Olivia Kim, Patrick G. Blachly, James Andrew McCammon
Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput. Biol. 11 (10) (2015)
Yinglong Miao, Ferran Feixas, Changsun Eun, James Andrew McCammon
Accelerated molecular dynamics simulations of protein folding. J. Comput. Chem. 36 (20) (2015)
Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon
AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. Comput. Phys. Commun. 184 (11) (2013)
Jacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon
Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. J. Chem. Inf. Model. 53 (7) (2013)
Meekyum Olivia Kim, Sara E. Nichols, Yi Wang, James Andrew McCammon
Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J. Comput. Aided Mol. Des. 27 (3) (2013)
Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon
into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations. PLoS Comput. Biol. 9 (7) (2013)
Patrick G. Blachly, César Augusto F. de Oliveira, Sarah L. Williams, James Andrew McCammon
Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs. PLoS Comput. Biol. 9 (12) (2013)
Jacob D. Durrant, James Andrew McCammon
. PLoS Comput. Biol. 8 (3) (2012)
Peter Michael Kekenes-Huskey, Steffen Lindert, James Andrew McCammon
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study. PLoS Comput. Biol. 8 (11) (2012)
Morgan Lawrenz, Jeff Wereszczynski, Juan Manuel Ortiz-Sánchez, Sara E. Nichols, James Andrew McCammon
Thermodynamic integration to predict host-guest binding affinities. J. Comput. Aided Mol. Des. 26 (5) (2012)
César Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, James Andrew McCammon
Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. PLoS Comput. Biol. 7 (10) (2011)
Sara E. Nichols, Riccardo Baron, Anthony Ivetac, James Andrew McCammon
Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. J. Chem. Inf. Model. 51 (6) (2011)
Denis Bucher, Barry J. Grant, Phineus R. Markwick, James Andrew McCammon
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics. PLoS Comput. Biol. 7 (4) (2011)
Julia Romanowska, James Andrew McCammon, Joanna Trylska
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. PLoS Comput. Biol. 7 (7) (2011)
Lars Skjaerven, Barry J. Grant, Arturo Muga, Knut Teigen, James Andrew McCammon, Nathalie Reuter, Aurora Martinez
Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. PLoS Comput. Biol. 7 (3) (2011)
Jacob D. Durrant, James Andrew McCammon
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inf. Model. 51 (11) (2011)
Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon
CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Inf. Model. 51 (10) (2011)
Suryani Lukman, Barry J. Grant, Alemayehu A. Gorfe, Guy H. Grant, James Andrew McCammon
The Distinct Conformational Dynamics of K-Ras and H-Ras A59G. PLoS Comput. Biol. 6 (9) (2010)
Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6 (1) (2010)
Jacob D. Durrant, James Andrew McCammon
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Inf. Model. 50 (10) (2010)
Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon
AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. Comput. Phys. Commun. 181 (6) (2010)
Gary A. Huber, James Andrew McCammon
Browndye: A software package for Brownian dynamics. Comput. Phys. Commun. 181 (11) (2010)
Yuhui Cheng, Zeyun Yu, Masahiko Hoshijima, Michael J. Holst, Andrew D. McCulloch, James Andrew McCammon, Anushka Michailova
Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum. PLoS Comput. Biol. 6 (10) (2010)
Jacob D. Durrant, James Andrew McCammon
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput. Biol. Chem. 34 (2) (2010)
Benzhuo Lu, Michael J. Holst, James Andrew McCammon, Yongcheng Zhou
Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions. J. Comput. Phys. 229 (19) (2010)
Arneh Babakhani, Todd T. Talley, Palmer Taylor, James Andrew McCammon
A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput. Biol. Chem. 33 (2) (2009)
Yuhui Cheng, Michael J. Holst, James Andrew McCammon
Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase. Pacific Symposium on Biocomputing (2009)
Mikolai Fajer, Robert V. Swift, James Andrew McCammon
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J. Comput. Chem. 30 (11) (2009)
Barry J. Grant, Alemayehu A. Gorfe, James Andrew McCammon
Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics. PLoS Comput. Biol. 5 (3) (2009)
Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine
Control of Cation Permeation through the Nicotinic Receptor Channel. PLoS Comput. Biol. 4 (2) (2008)
Rommie E. Amaro, Riccardo Baron, James Andrew McCammon
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. Aided Mol. Des. 22 (9) (2008)
Benzhuo Lu, Xiaolin Cheng, James Andrew McCammon
"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems. J. Comput. Phys. 226 (2) (2007)
Xiaolin Cheng, Hai-Long Wang, Barry J. Grant, Steven M. Sine, James Andrew McCammon
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors. PLoS Comput. Biol. 2 (9) (2006)
Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, James Andrew McCammon, Leo S. D. Caves
Bio3d: an R package for the comparative analysis of protein structures. Bioinform. 22 (21) (2006)
Kay Hamacher, Joanna Trylska, James Andrew McCammon
Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol. 2 (2) (2006)
Deqiang Zhang, James Andrew McCammon
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput. Biol. 1 (6) (2005)
Peter A. Sims, Chung F. Wong, Danka Vuga, James Andrew McCammon, Bartholomew M. Sefton
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J. Comput. Chem. 26 (7) (2005)
Todd J. Dolinsky, Jens E. Nielsen, James Andrew McCammon, Nathan A. Baker
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Peter A. Sims, Chung F. Wong, James Andrew McCammon
Charge optimization of the interface between protein kinases and their ligands. J. Comput. Chem. 25 (11) (2004)
Richard H. Henchman, James Andrew McCammon
Extracting hydration sites around proteins from explicit water simulations. J. Comput. Chem. 23 (9) (2002)
Tjerk P. Straatsma, James Andrew McCammon
Load balancing of molecular dynamics simulation with NWChem. IBM Syst. J. 40 (2) (2001)
Nathan A. Baker, David Sept, Michael J. Holst, James Andrew McCammon
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J. Res. Dev. 45 (3) (2001)
Michael J. Potter, Paul D. Kirchhoff, Heather A. Carlson, James Andrew McCammon
Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. J. Comput. Chem. 20 (9) (1999)
Piotr Bala, Pawel Grochowski, Krzysztof Nowinski, Terry W. Clark, Bogdan Lesyng, James Andrew McCammon
Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code. PARA (1998)
Piotr Bala, Terry W. Clark, Pawel Grochowski, Bogdan Lesyng, James Andrew McCammon
Parallel Version of a Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular Systems. PVM/MPI (1997)
Jan Antosiewicz, James M. Briggs, Adrian H. Elcock, Michael K. Gilson, James Andrew McCammon
Computing ionization states of proteins with a detailed charge model. J. Comput. Chem. 17 (14) (1996)
Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, James Andrew McCammon
A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. 16 (4) (1995)
Piotr Bala, Palo Grochowski, Bogdan Lesyng, James Andrew McCammon
Quantum-classical Molecular Dynamics and Its Computer Implementation. Comput. Chem. 19 (3) (1995)
Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked, James Andrew McCammon
I/O Limitations in Parallel Molecular Dynamics. SC (1995)
Micahel K. Golson, James Andrew McCammon, Jeffrey D. Madura
Molecular Dynamics Simulation with a Comtinuum Electrostatic Model of the Solvent. J. Comput. Chem. 16 (9) (1995)
Terry W. Clark, James Andrew McCammon, L. Ridgway Scott
Parallel Molecular Dynamics. PPSC (1991)
Michael J. Mitchell, James Andrew McCammon
Vector Optimization of Amber 3.0On the NEC SX-2/400Supercomputer. Comput. Chem. 15 (1) (1991)
Terry W. Clark, James Andrew McCammon
Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. Comput. Chem. 14 (3) (1990)
Terry P. Lybrand, James Andrew McCammon
Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. J. Comput. Aided Mol. Des. 2 (4) (1989)
J. C. Sauniere, Terry P. Lybrand, James Andrew McCammon, L. D. Pyle
Polarizable water models: Vectorization of energy calculations on the CYBER 205. Comput. Chem. 13 (4) (1989)
George L. Wilcox, Florante A. Quiocho, Cyrus Levinthal, Stephen C. Harvey, Gerald M. Maggiora, James Andrew McCammon
Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J. Comput. Aided Mol. Des. 1 (4) (1988)
Bhalachandra L. Tembre, James Andrew McCammon
Ligand-receptor interactions. Comput. Chem. 8 (4) (1984)
Stephen C. Harvey, James Andrew McCammon
Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles. Comput. Chem. 6 (4) (1982)