James Andrew McCammon - researchr alias

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Viewing Publication 1 - 64 from 64

2021

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main ProteaseTerra Sztain, Rommie E. Amaro, James Andrew McCammon. jcisd, 61(7):3495-3501, 2021. [doi]

2020

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometriesChristopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani. ploscb, 16(4), 2020. [doi]

2019

The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh GenerationChristopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst. TOMS, 45(3), 2019. [doi]

2018

Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body SimulationsFuhui Fang, Jingfang Huang, Gary A. Huber, James Andrew McCammon, Bo Zhang. siamsc, 40(3), 2018. [doi]

2015

2013

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial DrugsPatrick G. Blachly, César Augusto F. de Oliveira, Sarah L. Williams, James Andrew McCammon. ploscb, 9(12), 2013. [doi]

2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics SimulationsDenis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon. ploscb, 9(7), 2013. [doi]

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library ScreeningJacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon. jcisd, 53(7):1726-1735, 2013. [doi]

Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlCMeekyum Olivia Kim, Sara E. Nichols, Yi Wang 0015, James Andrew McCammon. jcamd, 27(3):235-246, 2013. [doi]

AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systemsBenzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon. cphysics, 184(11):2618-2619, 2013. [doi]

2012

in SilicoJacob D. Durrant, James Andrew McCammon. ploscb, 8(3), 2012. [doi]

Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation StudyPeter Michael Kekenes-Huskey, Steffen Lindert, James Andrew McCammon. ploscb, 8(11), 2012. [doi]

Thermodynamic integration to predict host-guest binding affinitiesMorgan Lawrenz, Jeff Wereszczynski, Juan Manuel Ortiz-Sánchez, Sara E. Nichols, James Andrew McCammon. jcamd, 26(5):569-576, 2012. [doi]

2011

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular DynamicsDenis Bucher, Barry J. Grant, Phineus R. Markwick, James Andrew McCammon. ploscb, 7(4), 2011. [doi]

Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics SimulationCésar Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, James Andrew McCammon. ploscb, 7(10), 2011. [doi]

NNScore 2.0: A Neural-Network Receptor-Ligand Scoring FunctionJacob D. Durrant, James Andrew McCammon. jcisd, 51(11):2897-2903, 2011. [doi]

CrystalDock: A Novel Approach to Fragment-Based Drug DesignJacob D. Durrant, Aaron J. Friedman, James Andrew McCammon. jcisd, 51(10):2573-2580, 2011. [doi]

Predictive Power of Molecular Dynamics Receptor Structures in Virtual ScreeningSara E. Nichols, Riccardo Baron, Anthony Ivetac, James Andrew McCammon. jcisd, 51(6):1439-1446, 2011. [doi]

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-SiteJulia Romanowska, James Andrew McCammon, Joanna Trylska. ploscb, 7(7), 2011. [doi]

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics SimulationsLars Skjaerven, Barry J. Grant, Arturo Muga, Knut Teigen, James Andrew McCammon, Nathalie Reuter, Aurora Martinez. ploscb, 7(3), 2011. [doi]

2010

2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic ReticulumYuhui Cheng, Zeyun Yu, Masahiko Hoshijima, Michael J. Holst, Andrew D. McCulloch, James Andrew McCammon, Anushka Michailova. ploscb, 6(10), 2010. [doi]

Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug designJacob D. Durrant, James Andrew McCammon. CANDC, 34(2):97-105, 2010. [doi]

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand ComplexesJacob D. Durrant, James Andrew McCammon. jcisd, 50(10):1865-1871, 2010. [doi]

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence HomologyJacob 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. ploscb, 6(1), 2010. [doi]

Browndye: A software package for Brownian dynamicsGary A. Huber, James Andrew McCammon. cphysics, 181(11):1896-1905, 2010. [doi]

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutionsBenzhuo Lu, Michael J. Holst, James Andrew McCammon, Y. C. Zhou. jcphy, 229(19):6979-6994, 2010. [doi]

The Distinct Conformational Dynamics of K-Ras and H-Ras A59GSuryani Lukman, Barry J. Grant, Alemayehu A. Gorfe, Guy H. Grant, James Andrew McCammon. ploscb, 6(9), 2010. [doi]

2009

A virtual screening study of the acetylcholine binding protein using a relaxed-complex approachArneh Babakhani, Todd T. Talley, Palmer Taylor, James Andrew McCammon. CANDC, 33(2):160-170, 2009. [doi]

Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 NeuraminidaseYuhui Cheng, Michael J. Holst, James Andrew McCammon. psb 2009: 281-292 [doi]

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular DynamicsBarry J. Grant, Alemayehu A. Gorfe, James Andrew McCammon. ploscb, 5(3), 2009. [doi]

2008

An improved relaxed complex scheme for receptor flexibility in computer-aided drug designRommie E. Amaro, Riccardo Baron, James Andrew McCammon. jcamd, 22(9):693-705, 2008. [doi]

Control of Cation Permeation through the Nicotinic Receptor ChannelHai Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine. ploscb, 4(2), 2008. [doi]

2007

"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systemsBenzhuo Lu, Xiaolin Cheng, James Andrew McCammon. jcphy, 226(2):1348-1366, 2007. [doi]

2006

Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic ReceptorsXiaolin Cheng, Hai Long Wang, Barry J. Grant, Steven M. Sine, James Andrew McCammon. ploscb, 2(9), 2006. [doi]

Dependency Map of Proteins in the Small Ribosomal SubunitKay Hamacher, Joanna Trylska, James Andrew McCammon. ploscb, 2(2), 2006. [doi]

2005

Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systemsPeter A. Sims, Chung F. Wong, Danka Vuga, James Andrew McCammon, Bartholomew M. Sefton. jcc, 26(7):668-681, 2005. [doi]

The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode AnalysisDeqiang Zhang, James Andrew McCammon. ploscb, 1(6), 2005. [doi]

2004

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculationsTodd J. Dolinsky, Jens E. Nielsen, James Andrew McCammon, Nathan A. Baker. nar, 32(Web-Server-Issue):665-667, 2004.

Charge optimization of the interface between protein kinases and their ligandsPeter A. Sims, Chung F. Wong, James Andrew McCammon. jcc, 25(11):1416-1429, 2004. [doi]

2002

Extracting hydration sites around proteins from explicit water simulationsRichard H. Henchman, James Andrew McCammon. jcc, 23(9):861-869, 2002. [doi]

2001

The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computersNathan A. Baker, David Sept, Michael J. Holst, James Andrew McCammon. ibmrd, 45(3):427-438, 2001. [doi]

Load balancing of molecular dynamics simulation with NWChemTjerk P. Straatsma, James Andrew McCammon. IBMSJ, 40(2):328-341, 2001. [doi]

1999

Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent SystemJan Antosiewicz, Elzbieta Blachut-Okrasinska, Tomasz Grycuk, James M. Briggs, Stanislaw T. Wlodek, Bogdan Lesyng, James Andrew McCammon. In Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas. Volume 4 of Lecture Notes in Computational Science and Engineering, pages 176-196, Springer, 1999. [doi]

Conformational Transitions of Proteins from Atomistic SimulationsVolkhard Helms, James Andrew McCammon. In Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas. Volume 4 of Lecture Notes in Computational Science and Engineering, pages 66-77, Springer, 1999. [doi]

Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent modelMichael J. Potter, Paul D. Kirchhoff, Heather A. Carlson, James Andrew McCammon. jcc, 20(9):956-970, 1999. [doi]

1998

Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics CodePiotr Bala, Pawel Grochowski, Krzysztof Nowinski, Terry W. Clark, Bogdan Lesyng, James Andrew McCammon. para 1998: 20-27

1997

Parallel Version of a Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular SystemsPiotr Bala, Terry W. Clark, Pawel Grochowski, Bogdan Lesyng, James Andrew McCammon. pvm 1997: 409-416

1996

Computing ionization states of proteins with a detailed charge modelJan Antosiewicz, James M. Briggs, Adrian H. Elcock, Michael K. Gilson, James Andrew McCammon. jcc, 17(14):1633-1644, 1996. [doi]

1995

1991

Parallel Molecular DynamicsTerry W. Clark, James Andrew McCammon, L. Ridgway Scott. ppsc 1992: 338-344

Vector Optimization of Amber 3.0On the NEC SX-2/400SupercomputerMichael J. Mitchell, James Andrew McCammon. CANDC, 15(1):79-85, 1991. [doi]

1990

Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architectureTerry W. Clark, James Andrew McCammon. CANDC, 14(3):219-224, 1990. [doi]

1989

Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirusTerry P. Lybrand, James Andrew McCammon. jcamd, 2(4):259-266, 1989. [doi]

Polarizable water models: Vectorization of energy calculations on the CYBER 205J. C. Sauniere, T. P. Lybrand, James Andrew McCammon, L. D. Pyle. CANDC, 13(4):313-317, 1989. [doi]

1988

Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and WaterGeorge L. Wilcox, Florante A. Quiocho, Cyrus Levinthal, Stephen C. Harvey, Gerald M. Maggiora, James Andrew McCammon. jcamd, 1(4):271-281, 1988. [doi]

1984

Ligand-receptor interactionsBhalachandra L. Tembre, James Andrew McCammon. CANDC, 8(4):281-283, 1984. [doi]

1982

Macromolecular conformational energy minimization: An algorithm varying pseudodihedral anglesStephen C. Harvey, James Andrew McCammon. CANDC, 6(4):173-179, 1982. [doi]

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