James Andrew McCammon

74 papers A 1Misc 1Journal 67Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	TimeStampEval: A Simple LLM Eval and a Little Fuzzy Matching Trick to Improve Search Accuracy. CoRR James Andrew McCammon
2024	J	`jnl`	NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J. Chem. Inf. Model. Andrew M. Stokely, Lane W. Votapka, Marcus T. Hock, Abigail E. Teitgen, James Andrew McCammon, Andrew D. McCulloch, Rommie E. Amaro
2024	J	`jnl`	Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome J. Chem. Inf. Model. Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, James Andrew McCammon
2021	J	`jnl`	Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J. Chem. Inf. Model. Terra Sztain, Rommie E. Amaro, James Andrew McCammon
2020	J	`jnl`	3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael J. Holst, Padmini Rangamani
2019	J	`jnl`	The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. ACM Trans. Math. Softw. Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
2018	J	`jnl`	Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J. Comput. Chem. Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, James Andrew McCammon, Ross C. Walker
2018	J	`jnl`	Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations. SIAM J. Sci. Comput. Fuhui Fang, Jingfang Huang, Gary A. Huber, James Andrew McCammon, Bo Zhang
2018	J	`jnl`	RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations. Comput. Phys. Commun. W. Guan, Xiaolin Cheng, J. Huang, G. Huber, Wei Li, James Andrew McCammon, Bo Zhang
2018	J	`jnl`	The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. CoRR Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
2017	J	`jnl`	RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. CoRR W. Guan, Xiaolin Cheng, J. Huang, G. Huber, Wei Li, James Andrew McCammon, Bo Zhang
2015	J	`jnl`	Accelerated molecular dynamics simulations of protein folding. J. Comput. Chem. Yinglong Miao, Ferran Feixas, Changsun Eun, James Andrew McCammon
2015	J	`jnl`	Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput. Biol. Meekyum Olivia Kim, Patrick G. Blachly, James Andrew McCammon
2015	J	`jnl`	In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J. Comput. Aided Mol. Des. Steffen Lindert, Lorillee Tallorin, Quynh G. Nguyen, Michael D. Burkart, James Andrew McCammon
2015	J	`jnl`	LS-VISM: A software package for analysis of biomolecular solvation. J. Comput. Chem. Shenggao Zhou, Li-Tien Cheng, Hui Sun, Jianwei Che, Joachim Dzubiella, Bo Li, James Andrew McCammon
2013	J	`jnl`	AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. Comput. Phys. Commun. Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon
2013	J	`jnl`	Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. J. Chem. Inf. Model. Jacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon
2013	J	`jnl`	Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J. Comput. Aided Mol. Des. Meekyum Olivia Kim, Sara E. Nichols, Yi Wang, James Andrew McCammon
2013	J	`jnl`	Insertion of the Ca PLoS Comput. Biol. Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon
2013	J	`jnl`	Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs. PLoS Comput. Biol. Patrick G. Blachly, César Augusto F. de Oliveira, Sarah L. Williams, James Andrew McCammon
2012	J	`jnl`	AutoClickChem: Click Chemistry PLoS Comput. Biol. Jacob D. Durrant, James Andrew McCammon
2012	J	`jnl`	Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study. PLoS Comput. Biol. Peter Michael Kekenes-Huskey, Steffen Lindert, James Andrew McCammon
2012	J	`jnl`	Thermodynamic integration to predict host-guest binding affinities. J. Comput. Aided Mol. Des. Morgan Lawrenz, Jeff Wereszczynski, Juan Manuel Ortiz-Sánchez, Sara E. Nichols, James Andrew McCammon
2011	J	`jnl`	Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics. PLoS Comput. Biol. Denis Bucher, Barry J. Grant, Phineus R. Markwick, James Andrew McCammon
2011	J	`jnl`	Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. PLoS Comput. Biol. Lars Skjaerven, Barry J. Grant, Arturo Muga, Knut Teigen, James Andrew McCammon, Nathalie Reuter, Aurora Martinez
2011	J	`jnl`	CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Inf. Model. Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon
2011	J	`jnl`	Large-Scale Conformational Changes of PLoS Comput. Biol. César Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, James Andrew McCammon
2011	J	`jnl`	NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inf. Model. Jacob D. Durrant, James Andrew McCammon
2011	J	`jnl`	Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. J. Chem. Inf. Model. Sara E. Nichols, Riccardo Baron, Anthony Ivetac, James Andrew McCammon
2011	J	`jnl`	Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. PLoS Comput. Biol. Julia Romanowska, James Andrew McCammon, Joanna Trylska
2010	J	`jnl`	A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 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
2010	J	`jnl`	AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. Comput. Phys. Commun. Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon
2010	J	`jnl`	Browndye: A software package for Brownian dynamics. Comput. Phys. Commun. Gary A. Huber, James Andrew McCammon
2010	J	`jnl`	NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Inf. Model. Jacob D. Durrant, James Andrew McCammon
2010	J	`jnl`	Numerical Analysis of Ca PLoS Comput. Biol. Yuhui Cheng, Zeyun Yu, Masahiko Hoshijima, Michael J. Holst, Andrew D. McCulloch, James Andrew McCammon, Anushka Michailova
2010	J	`jnl`	Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions. J. Comput. Phys. Benzhuo Lu, Michael J. Holst, James Andrew McCammon, Yongcheng Zhou
2010	J	`jnl`	Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput. Biol. Chem. Jacob D. Durrant, James Andrew McCammon
2010	J	`jnl`	The Distinct Conformational Dynamics of K-Ras and H-Ras A59G. PLoS Comput. Biol. Suryani Lukman, Barry J. Grant, Alemayehu A. Gorfe, Guy H. Grant, James Andrew McCammon
2009	J	`jnl`	A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput. Biol. Chem. Arneh Babakhani, Todd T. Talley, Palmer Taylor, James Andrew McCammon
2009	Misc	`conf`	Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase. Pacific Symposium on Biocomputing Yuhui Cheng, Michael J. Holst, James Andrew McCammon
2009	J	`jnl`	Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics. PLoS Comput. Biol. Barry J. Grant, Alemayehu A. Gorfe, James Andrew McCammon
2009	J	`jnl`	Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J. Comput. Chem. Mikolai Fajer, Robert V. Swift, James Andrew McCammon
2008	J	`jnl`	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. Aided Mol. Des. Rommie E. Amaro, Riccardo Baron, James Andrew McCammon
2008	J	`jnl`	Control of Cation Permeation through the Nicotinic Receptor Channel. PLoS Comput. Biol. Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine
2007	J	`jnl`	"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems. J. Comput. Phys. Benzhuo Lu, Xiaolin Cheng, James Andrew McCammon
2006	J	`jnl`	Bio3d: an R package for the comparative analysis of protein structures. Bioinform. Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, James Andrew McCammon, Leo S. D. Caves
2006	J	`jnl`	Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol. Kay Hamacher, Joanna Trylska, James Andrew McCammon
2006	J	`jnl`	Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors. PLoS Comput. Biol. Xiaolin Cheng, Hai-Long Wang, Barry J. Grant, Steven M. Sine, James Andrew McCammon
2005	J	`jnl`	Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J. Comput. Chem. Peter A. Sims, Chung F. Wong, Danka Vuga, James Andrew McCammon, Bartholomew M. Sefton
2005	J	`jnl`	The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput. Biol. Deqiang Zhang, James Andrew McCammon
2004	J	`jnl`	Charge optimization of the interface between protein kinases and their ligands. J. Comput. Chem. Peter A. Sims, Chung F. Wong, James Andrew McCammon
2004	J	`jnl`	Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem. John Mongan, David A. Case, James Andrew McCammon
2004	J	`jnl`	PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. Todd J. Dolinsky, Jens Erik Nielsen, James Andrew McCammon, Nathan A. Baker
2002	J	`jnl`	Extracting hydration sites around proteins from explicit water simulations. J. Comput. Chem. Richard H. Henchman, James Andrew McCammon
2001	J	`jnl`	Load balancing of molecular dynamics simulation with NWChem. IBM Syst. J. Tjerk P. Straatsma, James Andrew McCammon
2001	J	`jnl`	The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J. Res. Dev. Nathan A. Baker, David Sept, Michael J. Holst, James Andrew McCammon
1999	—	`ch.`	Conformational Transitions of Proteins from Atomistic Simulations. Computational Molecular Dynamics Volkhard Helms, James Andrew McCammon
1999	J	`jnl`	Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. J. Comput. Chem. Michael J. Potter, Paul D. Kirchhoff, Heather A. Carlson, James Andrew McCammon
1999	—	`ch.`	Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System. Computational Molecular Dynamics Jan Antosiewicz, Elzbieta Blachut-Okrasinska, Tomasz Grycuk, James M. Briggs, Stanislaw T. Wlodek, Bogdan Lesyng, James Andrew McCammon
1998	—	`conf`	Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code. PARA Piotr Bala, Pawel Grochowski, Krzysztof Nowinski, Terry W. Clark, Bogdan Lesyng, James Andrew McCammon
1997	—	`conf`	Parallel Version of a Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular Systems. PVM/MPI Piotr Bala, Terry W. Clark, Pawel Grochowski, Bogdan Lesyng, James Andrew McCammon
1996	J	`jnl`	Computing ionization states of proteins with a detailed charge model. J. Comput. Chem. Jan Antosiewicz, James M. Briggs, Adrian H. Elcock, Michael K. Gilson, James Andrew McCammon
1995	J	`jnl`	A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, James Andrew McCammon
1995	A	`conf`	I/O Limitations in Parallel Molecular Dynamics. SC Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked, James Andrew McCammon
1995	J	`jnl`	Molecular Dynamics Simulation with a Comtinuum Electrostatic Model of the Solvent. J. Comput. Chem. Micahel K. Golson, James Andrew McCammon, Jeffrey D. Madura
1995	J	`jnl`	Quantum-classical Molecular Dynamics and Its Computer Implementation. Comput. Chem. Piotr Bala, Palo Grochowski, Bogdan Lesyng, James Andrew McCammon
1991	—	`conf`	Parallel Molecular Dynamics. PP Terry W. Clark, James Andrew McCammon, L. Ridgway Scott
1991	J	`jnl`	Vector Optimization of Amber 3.0On the NEC SX-2/400Supercomputer. Comput. Chem. Michael J. Mitchell, James Andrew McCammon
1990	J	`jnl`	Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. Comput. Chem. Terry W. Clark, James Andrew McCammon
1989	J	`jnl`	Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. J. Comput. Aided Mol. Des. Terry P. Lybrand, James Andrew McCammon
1989	J	`jnl`	Polarizable water models: Vectorization of energy calculations on the CYBER 205. Comput. Chem. J. C. Sauniere, Terry P. Lybrand, James Andrew McCammon, L. D. Pyle
1988	J	`jnl`	Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J. Comput. Aided Mol. Des. George L. Wilcox, Florante A. Quiocho, Cyrus Levinthal, Stephen C. Harvey, Gerald M. Maggiora, James Andrew McCammon
1984	J	`jnl`	Ligand-receptor interactions. Comput. Chem. Bhalachandra L. Tembre, James Andrew McCammon
1982	J	`jnl`	Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles. Comput. Chem. Stephen C. Harvey, James Andrew McCammon