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ORCIDJames Andrew McCammon
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2020 – today
- 2024
[j64]Christian Seitz
, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, James Andrew McCammon:
Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. J. Chem. Inf. Model. 64(13): 5232-5241 (2024)- [j63]Andrew M. Stokely, Lane W. Votapka, Marcus T. Hock, Abigail E. Teitgen, James Andrew McCammon, Andrew D. McCulloch, Rommie E. Amaro:
NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J. Chem. Inf. Model. 64(20): 7966-7976 (2024) - 2021
- [j62]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): 3495-3501 (2021) - 2020
- [j61]Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael J. Holst, Padmini Rangamani:
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j60]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): 28:1-28:20 (2019) - 2018
- [j59]W. Guan, Xiaolin 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: 99-108 (2018) - [j58]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): 1354-1358 (2018) - [j57]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) - [i2]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. CoRR abs/1807.01417 (2018) - 2017
- [i1]W. Guan, Xiaolin 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 abs/1711.02976 (2017) - 2015
- [j56]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): 79-87 (2015) - [j55]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): 1047-1059 (2015) - [j54]Yinglong Miao, Ferran Feixas, Changsun Eun, James Andrew McCammon:
Accelerated molecular dynamics simulations of protein folding. J. Comput. Chem. 36(20): 1536-1549 (2015) - [j53]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) - 2013
- [j52]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): 2618-2619 (2013) - [j51]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): 235-246 (2013) - [j50]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): 1726-1735 (2013) - [j49]Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon:
Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations. PLoS Comput. Biol. 9(7) (2013) - [j48]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) - 2012
- [j47]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): 569-576 (2012) - [j46]Jacob D. Durrant, James Andrew McCammon:
AutoClickChem: Click Chemistry in Silico. PLoS Comput. Biol. 8(3) (2012) - [j45]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) - 2011
- [j44]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): 1439-1446 (2011) - [j43]Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon:
CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Inf. Model. 51(10): 2573-2580 (2011) - [j42]Jacob D. Durrant, James Andrew McCammon:
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inf. Model. 51(11): 2897-2903 (2011) - [j41]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) - [j40]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) - [j39]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) - [j38]César Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, James Andrew McCammon:
Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. PLoS Comput. Biol. 7(10) (2011) - 2010
- [j37]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): 97-105 (2010) - [j36]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): 1150-1160 (2010) - [j35]Gary A. Huber, James Andrew McCammon:
Browndye: A software package for Brownian dynamics. Comput. Phys. Commun. 181(11): 1896-1905 (2010) - [j34]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): 1865-1871 (2010) - [j33]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): 6979-6994 (2010) - [j32]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) - [j31]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) - [j30]Yuhui Cheng, Zeyun Yu, Masahiko Hoshijima, Michael J. Holst, Andrew D. McCulloch, James Andrew McCammon, Anushka Michailova:
Numerical Analysis of Ca2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum. PLoS Comput. Biol. 6(10) (2010)
2000 – 2009
- 2009
- [j29]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): 160-170 (2009) - [j28]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): 1719-1725 (2009) - [j27]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) - [c5]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: 281-292 - 2008
- [j26]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): 693-705 (2008) - [j25]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) - 2007
- [j24]Benzhuo Lu, Xiaolin Cheng, James Andrew McCammon:
"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems. J. Comput. Phys. 226(2): 1348-1366 (2007) - 2006
- [j23]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): 2695-2696 (2006) - [j22]Kay Hamacher, Joanna Trylska, James Andrew McCammon:
Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol. 2(2) (2006) - [j21]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) - 2005
- [j20]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): 668-681 (2005) - [j19]Deqiang Zhang, James Andrew McCammon:
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput. Biol. 1(6) (2005) - 2004
- [j18]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): 1416-1429 (2004) - [j17]John Mongan, David A. Case, James Andrew McCammon:
Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem. 25(16): 2038-2048 (2004) - [j16]Todd J. Dolinsky, Jens Erik 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): 665-667 (2004) - 2002
- [j15]Richard H. Henchman, James Andrew McCammon:
Extracting hydration sites around proteins from explicit water simulations. J. Comput. Chem. 23(9): 861-869 (2002) - 2001
- [j14]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): 427-438 (2001) - [j13]Tjerk P. Straatsma, James Andrew McCammon:
Load balancing of molecular dynamics simulation with NWChem. IBM Syst. J. 40(2): 328-341 (2001)
1990 – 1999
- 1999
- [j12]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): 956-970 (1999) - [p2]Volkhard Helms, James Andrew McCammon:
Conformational Transitions of Proteins from Atomistic Simulations. Computational Molecular Dynamics 1999: 66-77 - [p1]Jan Antosiewicz, Elzbieta Blachut-Okrasinska, Tomasz Grycuk, James M. Briggs, Stanislaw T. Wlodek, Bogdan Lesyng, James Andrew McCammon:
Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System. Computational Molecular Dynamics 1999: 176-196 - 1998
- [c4]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: 20-27 - 1997
- [c3]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: 409-416 - 1996
- [j11]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): 1633-1644 (1996) - 1995
- [j10]Piotr Bala, Palo Grochowski, Bogdan Lesyng, James Andrew McCammon:
Quantum-classical Molecular Dynamics and Its Computer Implementation. Comput. Chem. 19(3): 155-160 (1995) - [j9]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): 454-464 (1995) - [j8]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): 1081-1095 (1995) - [c2]Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked, James Andrew McCammon:
I/O Limitations in Parallel Molecular Dynamics. SC 1995: 23 - 1991
- [j7]Michael J. Mitchell, James Andrew McCammon:
Vector Optimization of Amber 3.0On the NEC SX-2/400Supercomputer. Comput. Chem. 15(1): 79-85 (1991) - [c1]Terry W. Clark, James Andrew McCammon, L. Ridgway Scott:
Parallel Molecular Dynamics. PP 1991: 338-344 - 1990
- [j6]Terry W. Clark, James Andrew McCammon:
Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. Comput. Chem. 14(3): 219-224 (1990)
1980 – 1989
- 1989
- [j5]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): 313-317 (1989) - [j4]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): 259-266 (1989) - 1988
- [j3]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): 271-281 (1988) - 1984
- [j2]Bhalachandra L. Tembre, James Andrew McCammon:
Ligand-receptor interactions. Comput. Chem. 8(4): 281-283 (1984) - 1982
- [j1]Stephen C. Harvey, James Andrew McCammon:
Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles. Comput. Chem. 6(4): 173-179 (1982)
Coauthor Index
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