Author details

Full Name

James Andrew McCammon

Affiliation

ORCID

Career Start Year

1972

Papers

630

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37043829	Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors.	ACS Chem Biol	2023
37671411	Interface Engineering of Carrier-Protein-Dependent Metabolic Pathways.		2023
37601331	Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling.	J Appl Phys	2023
37745347	Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.		2023
38014187	Dilated cardiomyopathy mutation in beta-cardiac myosin enhances actin activation of the power stroke and phosphate release.		2023
37903229	Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.		2023
37207626	PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period.		2023
36733435	Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning.		2023
34996868	Lipoprotein-associated phospholipase A: A paradigm for allosteric regulation by membranes.	Proceedings of the National Academy of Sciences of the United States of America	2022
36173802	Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition.	ACS Chemical Biology	2022
35755809	Investigating Intrinsically Disordered Proteins With Brownian Dynamics.	Frontiers in Molecular Biosciences	2022
35922510	Architecture and self-assembly of the jumbo bacteriophage nuclear shell.	Nature	2022
36475789	Stomatal CO/bicarbonate sensor consists of two interacting protein kinases, Raf-like HT1 and non-kinase-activity requiring MPK12/MPK4.		2022
34413500	A glycan gate controls opening of the SARS-CoV-2 spike protein.	Nat Chem	2021
34241191	Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RIÎ± liquid-liquid phase separation.	J Chem Phys	2021
33846262	Decoding allosteric regulation by the acyl carrier protein.	Proceedings of the National Academy of Sciences of the United States of America	2021
33782130	The myosin II coiled-coil domain atomic structure in its native environment.	Proceedings of the National Academy of Sciences of the United States of America	2021
33619492	A glycan gate controls opening of the SARS-CoV-2 spike protein.	bioRxiv	2021
33939913	Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease.	J Chem Inf Model	2021
33650860	Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.	Journal of Chemical Theory and Computation	2021
34621930	Data for molecular dynamics simulations of cytochrome oxidase with the Amber force field.	Data in Brief	2021
34844409	Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.	J Chem Theory Comput	2021
32743587	Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease.	bioRxiv	2020
32251448	3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.	PLoS Comput Biol	2020
32032503	An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.	Biophys J	2020
32929027	Interfacial plasticity facilitates high reaction rate of FAS malonyl-CoA:ACP transacylase, FabD.	Proceedings of the National Academy of Sciences of the United States of America	2020
30880083	Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.	Journal of Structural Biology	2019
32309795	Brownian Dynamics Simulations of Biological Molecules.	Trends in Chemistry	2019
30606449	Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.	Biophys J	2019
30264484	pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study.	Journal of Molecular Recognition	2019
30194895	Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases.	ChemBioChem	2019
30570806	Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria.	Chem Biol Drug Des	2019
31041385	Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.	ACS Cent Sci	2019
31511751	The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution.	Physics Today	2019
31140212	Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein.	Angewandte Chemie - International Edition	2019
30872475	Structural and dynamical rationale for fatty acid unsaturation in .	Proceedings of the National Academy of Sciences of the United States of America	2019
31474782	The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation.	ACM Trans Math Softw	2019
31397556	Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins.	Biochemistry	2019
31547973	A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics.	Biophys J	2019
31452593	HIERARCHICAL ORTHOGONAL MATRIX GENERATION AND MATRIX-VECTOR MULTIPLICATIONS IN RIGID BODY SIMULATIONS.	SIAM Journal of Scientific Computing	2018
28639411	Mapping the allosteric sites of the A adenosine receptor.		2018
28836357	Improvements to the APBS biomolecular solvation software suite.	Protein Science	2018
30555184	Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.	Q Rev Biophys	2018
30301791	Identification of SLAC1 anion channel residues required for CO/bicarbonate sensing and regulation of stomatal movements.	Proceedings of the National Academy of Sciences of the United States of America	2018
30252476	Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations.	Journal of Physical Chemistry B	2018
30147116	RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations.	Computer Physics Communications	2018
30282755	A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from with Fungal Membranes via Its Î³-Core Motif.	mSphere	2018
29532496	Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.	Journal of Computational Chemistry	2018
29489349	Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.	Journal of Chemical Theory and Computation	2018
29094409	Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.	Protein Science	2018