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

per Swails, Jason M., York, Darrin M., Roitberg, Adrian E.
Publicat 2014

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

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

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

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

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

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

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

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

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

per 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.
Publicat a Biophys J (2015)

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

per 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
Publicat a J Chem Theory Comput (2015)