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Jason M. Swails, Ph.D.

Affiliations: 
2013 University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Physical Chemistry, Theory Physics, Molecular Chemistry
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Adrian Enrique Roitberg grad student 2013 UF Gainesville
 (Free energy simulations of complex biological systems at constant pH.)

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Case DA, Aktulga HM, Belfon K, et al. (2023) AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191
Moriarty NW, Janowski PA, Swails JM, et al. (2020) Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallographica. Section D, Structural Biology. 76: 51-62
Liu J, Swails J, Zhang JZH, et al. (2018) A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. Journal of the American Chemical Society
Yeager AV, Swails JM, Miller Iii BR. (2017) Improved accuracy for constant pH-REMD simulations through modification of carboxylate effective radii. Journal of Chemical Theory and Computation
Eastman P, Swails J, Chodera JD, et al. (2017) OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659
Shirts MR, Klein C, Swails JM, et al. (2016) Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design
Albaugh A, Boateng HA, Bradshaw RT, et al. (2016) Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B
Lee J, Cheng X, Swails JM, et al. (2015) CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation
McGibbon RT, Beauchamp KA, Harrigan MP, et al. (2015) MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal. 109: 1528-32
Swails J, Zhu T, He X, et al. (2015) AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Journal of Biomolecular Nmr. 63: 125-39
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