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

Por Swails, Jason M., York, Darrin M., Roitberg, Adrian E.
Publicado em 2014

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

Por Swails, Jason M., Meng, Yilin, Walker, F. Ann, Marti, Marcelo A., Estrin, Dario A., Roitberg, Adrian E.
Publicado em 2009

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

Por Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Swails, Jason M., Roitberg, Adrian E., Cheatham, Thomas E.
Publicado em 2013

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

Por Moriarty, Nigel W., Janowski, Pawel A., Swails, Jason M., Nguyen, Hai, Richardson, Jane S., Case, David A., Adams, Paul D.
Publicado no Acta Crystallogr D Struct Biol (2020)

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Por Shirts, Michael R., Klein, Christoph, Swails, Jason M., Yin, Jian, Gilson, Michael K., Mobley, David L., Case, David A., Zhong, Ellen D.
Publicado no J Comput Aided Mol Des (2016)

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

Por 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.
Publicado no Biophys J (2015)

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

Por 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
Publicado no J Chem Theory Comput (2015)