Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

od Swails, Jason M., York, Darrin M., Roitberg, Adrian E.
Izdano 2014

pH Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

od Swails, Jason M., Meng, Yilin, Walker, F. Ann, Marti, Marcelo A., Estrin, Dario A., Roitberg, Adrian E.
Izdano 2009

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

od Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Swails, Jason M., Roitberg, Adrian E., Cheatham, Thomas E.
Izdano 2013

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

od Moriarty, Nigel W., Janowski, Pawel A., Swails, Jason M., Nguyen, Hai, Richardson, Jane S., Case, David A., Adams, Paul D.
izdano v Acta Crystallogr D Struct Biol (2020)

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

od Shirts, Michael R., Klein, Christoph, Swails, Jason M., Yin, Jian, Gilson, Michael K., Mobley, David L., Case, David A., Zhong, Ellen D.
izdano v J Comput Aided Mol Des (2016)

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

od McGibbon, Robert T., Beauchamp, Kyle A., Harrigan, Matthew P., Klein, Christoph, Swails, Jason M., Hernández, Carlos X., Schwantes, Christian R., Wang, Lee-Ping, Lane, Thomas J., Pande, Vijay S.
izdano v Biophys J (2015)

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

od Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., Im, Wonpil
izdano v J Chem Theory Comput (2015)