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James Andrew McCammon
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2020 – today
- 2024
- [j63]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) - 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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