James Andrew McCammon
Orcid: 0000-0003-3065-1456
According to our database1,
James Andrew McCammon
authored at least 68 papers
between 1982 and 2021.
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Bibliography
2021
J. Chem. Inf. Model., 2021
2020
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.
PLoS Comput. Biol., 2020
2019
The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation.
ACM Trans. Math. Softw., 2019
2018
Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations.
SIAM J. Sci. Comput., 2018
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.
J. Comput. Chem., 2018
RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations.
Comput. Phys. Commun., 2018
2015
Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.
PLoS Comput. Biol., 2015
J. Comput. Chem., 2015
J. Comput. Chem., 2015
J. Comput. Aided Mol. Des., 2015
2013
Insertion of the Ca<sup>2+</sup>-Independent Phospholipase A<sub>2</sub> into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations.
PLoS Comput. Biol., 2013
Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs.
PLoS Comput. Biol., 2013
Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening.
J. Chem. Inf. Model., 2013
Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC.
J. Comput. Aided Mol. Des., 2013
AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems.
Comput. Phys. Commun., 2013
2012
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study.
PLoS Comput. Biol., 2012
J. Comput. Aided Mol. Des., 2012
2011
Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations.
PLoS Comput. Biol., 2011
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site.
PLoS Comput. Biol., 2011
Large-Scale Conformational Changes of <i>Trypanosoma cruzi</i> Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation.
PLoS Comput. Biol., 2011
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics.
PLoS Comput. Biol., 2011
J. Chem. Inf. Model., 2011
J. Chem. Inf. Model., 2011
J. Chem. Inf. Model., 2011
2010
PLoS Comput. Biol., 2010
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
PLoS Comput. Biol., 2010
Numerical Analysis of Ca<sup>2+</sup> Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum.
PLoS Comput. Biol., 2010
Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions.
J. Comput. Phys., 2010
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes.
J. Chem. Inf. Model., 2010
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design.
Comput. Biol. Chem., 2010
2009
Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics.
PLoS Comput. Biol., 2009
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics.
J. Comput. Chem., 2009
A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.
Comput. Biol. Chem., 2009
Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
2008
PLoS Comput. Biol., 2008
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
J. Comput. Aided Mol. Des., 2008
2007
"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems.
J. Comput. Phys., 2007
2006
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors.
PLoS Comput. Biol., 2006
Bioinform., 2006
2005
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis.
PLoS Comput. Biol., 2005
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems.
J. Comput. Chem., 2005
2004
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Res., 2004
J. Comput. Chem., 2004
J. Comput. Chem., 2004
2002
J. Comput. Chem., 2002
2001
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers.
IBM J. Res. Dev., 2001
1999
Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model.
J. Comput. Chem., 1999
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999
Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System.
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999
1998
Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code.
Proceedings of the Applied Parallel Computing, 1998
1997
Parallel Version of a Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular Systems.
Proceedings of the Recent Advances in Parallel Virtual Machine and Message Passing Interface, 1997
1996
J. Comput. Chem., 1996
1995
J. Comput. Chem., 1995
J. Comput. Chem., 1995
Comput. Chem., 1995
Proceedings of the Proceedings Supercomputing '95, San Diego, CA, USA, December 4-8, 1995, 1995
1991
Comput. Chem., 1991
Parallel Molecular Dynamics.
Proceedings of the Fifth SIAM Conference on Parallel Processing for Scientific Computing, 1991
1990
Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture.
Comput. Chem., 1990
1989
Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus.
J. Comput. Aided Mol. Des., 1989
Comput. Chem., 1989
1988
Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water.
J. Comput. Aided Mol. Des., 1988
1984
1982
Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles.
Comput. Chem., 1982