Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles. - Stephen C. Harvey; James Andrew McCammon (Comput. Chem., 1982)

Ligand-receptor interactions. - Bhalachandra L. Tembre; James Andrew McCammon (Comput. Chem., 1984)

Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. - George L. Wilcox; Florante A. Quiocho; Cyrus Levinthal; Stephen C. Harvey; Gerald M. Maggiora; James Andrew McCammon (J. Comput. Aided Mol. Des., 1988)

Polarizable water models: Vectorization of energy calculations on the CYBER 205. - J. C. Sauniere; Terry P. Lybrand; James Andrew McCammon; L. D. Pyle (Comput. Chem., 1989)

Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. - Terry P. Lybrand; James Andrew McCammon (J. Comput. Aided Mol. Des., 1989)

Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. - Terry W. Clark; James Andrew McCammon (Comput. Chem., 1990)

Parallel Molecular Dynamics. - Terry W. Clark; James Andrew McCammon; L. Ridgway Scott (PP, 1991)

Vector Optimization of Amber 3.0On the NEC SX-2/400Supercomputer. - Michael J. Mitchell; James Andrew McCammon (Comput. Chem., 1991)

I/O Limitations in Parallel Molecular Dynamics. - Terry W. Clark; L. Ridgway Scott; Stanislaw Wloked; James Andrew McCammon (SC, 1995)

Quantum-classical Molecular Dynamics and Its Computer Implementation. - Piotr Bala; Palo Grochowski; Bogdan Lesyng; James Andrew McCammon (Comput. Chem., 1995)

Molecular Dynamics Simulation with a Comtinuum Electrostatic Model of the Solvent. - Micahel K. Golson; James Andrew McCammon; Jeffrey D. Madura (J. Comput. Chem., 1995)

A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. - Brock A. Luty; Zelda R. Wasserman; Pieter F. W. Stouten; C. Nicholas Hodge; Martin Zacharias; James Andrew McCammon (J. Comput. Chem., 1995)

Computing ionization states of proteins with a detailed charge model. - Jan Antosiewicz; James M. Briggs; Adrian H. Elcock; Michael K. Gilson; James Andrew McCammon (J. Comput. Chem., 1996)

Parallel Version of a Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular Systems. - Piotr Bala; Terry W. Clark; Pawel Grochowski; Bogdan Lesyng; James Andrew McCammon (PVM/MPI, 1997)

Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code. - Piotr Bala; Pawel Grochowski; Krzysztof Nowinski; Terry W. Clark; Bogdan Lesyng; James Andrew McCammon (PARA, 1998)

Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System. - Jan Antosiewicz; Elzbieta Blachut-Okrasinska; Tomasz Grycuk; James M. Briggs; Stanislaw T. Wlodek; Bogdan Lesyng; James Andrew McCammon (Computational Molecular Dynamics, 1999)

Conformational Transitions of Proteins from Atomistic Simulations. - Volkhard Helms; James Andrew McCammon (Computational Molecular Dynamics, 1999)

Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. - Michael J. Potter; Paul D. Kirchhoff; Heather A. Carlson; James Andrew McCammon (J. Comput. Chem., 1999)

The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. - Nathan A. Baker; David Sept; Michael J. Holst; James Andrew McCammon (IBM J. Res. Dev., 2001)

Load balancing of molecular dynamics simulation with NWChem. - Tjerk P. Straatsma; James Andrew McCammon (IBM Syst. J., 2001)

Extracting hydration sites around proteins from explicit water simulations. - Richard H. Henchman; James Andrew McCammon (J. Comput. Chem., 2002)

Constant pH molecular dynamics in generalized Born implicit solvent. - John Mongan; David A. Case; James Andrew McCammon (J. Comput. Chem., 2004)

Charge optimization of the interface between protein kinases and their ligands. - Peter A. Sims; Chung F. Wong; James Andrew McCammon (J. Comput. Chem., 2004)

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. - Todd J. Dolinsky; Jens Erik Nielsen; James Andrew McCammon; Nathan A. Baker (Nucleic Acids Res., 2004)

Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. - Peter A. Sims; Chung F. Wong; Danka Vuga; James Andrew McCammon; Bartholomew M. Sefton (J. Comput. Chem., 2005)

The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. - Deqiang Zhang; James Andrew McCammon (PLoS Comput. Biol., 2005)

Bio3d: an R package for the comparative analysis of protein structures. - Barry J. Grant; Ana P. C. Rodrigues; Karim M. ElSawy; James Andrew McCammon; Leo S. D. Caves (Bioinform., 2006)

Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors. - Xiaolin Cheng; Hai-Long Wang; Barry J. Grant; Steven M. Sine; James Andrew McCammon (PLoS Comput. Biol., 2006)

Dependency Map of Proteins in the Small Ribosomal Subunit. - Kay Hamacher; Joanna Trylska; James Andrew McCammon (PLoS Comput. Biol., 2006)

"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems. - Benzhuo Lu; Xiaolin Cheng; James Andrew McCammon (J. Comput. Phys., 2007)

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. - Rommie E. Amaro; Riccardo Baron; James Andrew McCammon (J. Comput. Aided Mol. Des., 2008)

Control of Cation Permeation through the Nicotinic Receptor Channel. - Hai-Long Wang; Xiaolin Cheng; Palmer Taylor; James Andrew McCammon; Steven M. Sine (PLoS Comput. Biol., 2008)

Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase. - Yuhui Cheng; Michael J. Holst; James Andrew McCammon (Pacific Symposium on Biocomputing, 2009)

A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. - Arneh Babakhani; Todd T. Talley; Palmer Taylor; James Andrew McCammon (Comput. Biol. Chem., 2009)

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. - Mikolai Fajer; Robert V. Swift; James Andrew McCammon (J. Comput. Chem., 2009)

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics. - Barry J. Grant; Alemayehu A. Gorfe; James Andrew McCammon (PLoS Comput. Biol., 2009)

Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. - Jacob D. Durrant; James Andrew McCammon (Comput. Biol. Chem., 2010)

Browndye: A software package for Brownian dynamics. - Gary A. Huber; James Andrew McCammon (Comput. Phys. Commun., 2010)

AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. - Benzhuo Lu; Xiaolin Cheng; Jingfang Huang; James Andrew McCammon (Comput. Phys. Commun., 2010)

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. - Jacob D. Durrant; James Andrew McCammon (J. Chem. Inf. Model., 2010)

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions. - Benzhuo Lu; Michael J. Holst; James Andrew McCammon; Yongcheng Zhou (J. Comput. Phys., 2010)

Numerical Analysis of Ca2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum. - Yuhui Cheng; Zeyun Yu; Masahiko Hoshijima; Michael J. Holst; Andrew D. McCulloch; James Andrew McCammon; Anushka Michailova (PLoS Comput. Biol., 2010)

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. - Jacob D. Durrant; Rommie E. Amaro; Lei Xie 006; Michael D. Urbaniak; Michael A. J. Ferguson; Antti Haapalainen; Zhijun Chen; Anne Marie Di Guilmi; Frank Wunder; Philip E. Bourne; James Andrew McCammon (PLoS Comput. Biol., 2010)

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G. - Suryani Lukman; Barry J. Grant; Alemayehu A. Gorfe; Guy H. Grant; James Andrew McCammon (PLoS Comput. Biol., 2010)

CrystalDock: A Novel Approach to Fragment-Based Drug Design. - Jacob D. Durrant; Aaron J. Friedman; James Andrew McCammon (J. Chem. Inf. Model., 2011)

NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. - Jacob D. Durrant; James Andrew McCammon (J. Chem. Inf. Model., 2011)

Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. - Sara E. Nichols; Riccardo Baron; Anthony Ivetac; James Andrew McCammon (J. Chem. Inf. Model., 2011)

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics. - Denis Bucher; Barry J. Grant; Phineus R. Markwick; James Andrew McCammon (PLoS Comput. Biol., 2011)

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. - César Augusto F. de Oliveira; Barry J. Grant; Michelle Zhou; James Andrew McCammon (PLoS Comput. Biol., 2011)

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. - Julia Romanowska; James Andrew McCammon; Joanna Trylska (PLoS Comput. Biol., 2011)

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. - Lars Skjaerven; Barry J. Grant; Arturo Muga; Knut Teigen; James Andrew McCammon; Nathalie Reuter; Aurora Martinez (PLoS Comput. Biol., 2011)

Thermodynamic integration to predict host-guest binding affinities. - Morgan Lawrenz; Jeff Wereszczynski; Juan Manuel Ortiz-Sánchez; Sara E. Nichols; James Andrew McCammon (J. Comput. Aided Mol. Des., 2012)

AutoClickChem: Click Chemistry in Silico. - Jacob D. Durrant; James Andrew McCammon (PLoS Comput. Biol., 2012)

Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study. - Peter Michael Kekenes-Huskey; Steffen Lindert; James Andrew McCammon (PLoS Comput. Biol., 2012)

Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. - Meekyum Olivia Kim; Sara E. Nichols; Yi Wang 015; James Andrew McCammon (J. Comput. Aided Mol. Des., 2013)

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. - Jacob D. Durrant; Aaron J. Friedman; Kathleen Roger; James Andrew McCammon (J. Chem. Inf. Model., 2013)

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs. - Patrick G. Blachly; César Augusto F. de Oliveira; Sarah L. Williams; James Andrew McCammon (PLoS Comput. Biol., 2013)

Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations. - Denis Bucher; Yuan-Hao Hsu; Varnavas D. Mouchlis; Edward A. Dennis; James Andrew McCammon (PLoS Comput. Biol., 2013)

In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. - Steffen Lindert; Lorillee Tallorin; Quynh G. Nguyen; Michael D. Burkart; James Andrew McCammon (J. Comput. Aided Mol. Des., 2015)

Accelerated molecular dynamics simulations of protein folding. - Yinglong Miao; Ferran Feixas; Changsun Eun; James Andrew McCammon (J. Comput. Chem., 2015)

LS-VISM: A software package for analysis of biomolecular solvation. - Shenggao Zhou; Li-Tien Cheng; Hui Sun; Jianwei Che; Joachim Dzubiella; Bo Li 007; James Andrew McCammon (J. Comput. Chem., 2015)

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. - Meekyum Olivia Kim; Patrick G. Blachly; James Andrew McCammon (PLoS Comput. Biol., 2015)

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations. - W. Guan; Xiaolin Cheng; J. Huang; G. Huber; Wei Li; James Andrew McCammon; Bo Zhang (Comput. Phys. Commun., 2018)

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. - Daniel J. Mermelstein; Charles Lin; Gard Nelson; Rachael Kretsch; James Andrew McCammon; Ross C. Walker (J. Comput. Chem., 2018)

Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations. - Fuhui Fang; Jingfang Huang; Gary A. Huber; James Andrew McCammon; Bo Zhang (SIAM J. Sci. Comput., 2018)

The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. - Christopher T. Lee; John B. Moody; Rommie E. Amaro; James Andrew McCammon; Michael J. Holst (ACM Trans. Math. Softw., 2019)

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. - Christopher T. Lee; Justin G. Laughlin; Nils Angliviel de La Beaumelle; Rommie E. Amaro; James Andrew McCammon; Ravi Ramamoorthi; Michael J. Holst; Padmini Rangamani (PLoS Comput. Biol., 2020)

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. - Terra Sztain; Rommie E. Amaro; James Andrew McCammon (J. Chem. Inf. Model., 2021)

Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. - Christian Seitz; Surl-Hee Ahn; Haixin Wei; Matson Kyte; Gregory M. Cook; Kurt L. Krause; James Andrew McCammon (J. Chem. Inf. Model., 2024)

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. - Andrew M. Stokely; Lane W. Votapka; Marcus T. Hock; Abigail E. Teitgen; James Andrew McCammon; Andrew D. McCulloch; Rommie E. Amaro (J. Chem. Inf. Model., 2024)