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Jason M. Swails · SciRah

Researcher profile · Semantic Scholar

Jason M. Swails

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Jason M. Swails — researcher profile on SciRah

h-index: 20
Works: 30
Citations: 16K

Most-cited papers

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R. Miller, T. D. McGee, Jason M. Swails, Nadine Homeyer +2 more
2012Journal of Chemical Theory and Computation4,297 citations
Semantic Scholar
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
Ju-Min Lee, Xi Cheng, Jason M. Swails, M. S. Yeom +13 more
2015Journal of Chemical Theory and Computation4,188 citations Open access
Semantic Scholar
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
P. Eastman, Jason M. Swails, J. Chodera, R. McGibbon +9 more
2016bioRxiv2,642 citations Open access
Semantic Scholar
MDTraj: a modern, open library for the analysis of molecular dynamics trajectories
R. McGibbon, K. Beauchamp, M. Harrigan, Christoph Klein +6 more
2014bioRxiv2,346 citations Open access
Semantic Scholar
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials
Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, C. Abreu +21 more
2023Journal of Physical Chemistry B425 citations Open access
Semantic Scholar
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
M. Shirts, Christoph Klein, Jason M. Swails, Jian Yin +4 more
2016bioRxiv359 citations Open access
Semantic Scholar
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
Jason M. Swails, D. York, A. Roitberg
2014Journal of Chemical Theory and Computation255 citations Open access
Semantic Scholar
Recent Developments in Amber Biomolecular Simulations
David A. Case, D. Cerutti, Vinícius Wilian D Cruzeiro, Thomas A. Darden +27 more
2025Journal of Chemical Information and Modeling238 citations Open access
Semantic Scholar
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials
Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, C. Abreu +21 more
2023arXiv.org223 citations Open access
Semantic Scholar
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
Christina Bergonzo, N. M. Henriksen, D. Roe, Jason M. Swails +2 more
2013Journal of Chemical Theory and Computation123 citations Open access
Semantic Scholar
Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics.
Jason M. Swails, A. Roitberg
2012Journal of Chemical Theory and Computation103 citations
Semantic Scholar
Advanced Potential Energy Surfaces for Molecular Simulation
Alex Albaugh, Henry A. Boateng, Richard T. Bradshaw, Omar N. A. Demerdash +17 more
2016Journal of Physical Chemistry B80 citations Open access
Semantic Scholar
MMPBSA . py : An E ffi cient Program for End-State Free Energy Calculations
Bill R. Miller, T. D. McGee, Jason M. Swails, Nadine Homeyer +2 more
201276 citations
Semantic Scholar
AFNMR: Automated Fragmentation Quantum mechanical Calculation of NMR Chemical shifts for Biomolecules
Jason M. Swails, T. Zhu, Xiao He, D. Case
2015Journal of Biomolecular NMR58 citations Open access
Semantic Scholar
SPAM: A Simple Approach for Profiling Bound Water Molecules.
Guanglei Cui, Jason M. Swails, E. Manas
2013Journal of Chemical Theory and Computation45 citations
Semantic Scholar
Interpretation of pH-activity Profiles for Acid-Base Catalysis from Molecular Simulations
Thakshila Dissanayake, Jason M. Swails, M. Harris, A. Roitberg +1 more
2015Biochemistry41 citations Open access
Semantic Scholar
Amber 2015, University of California, San Francisco
D. Case, J. Berryman, Robin M. Betz, D. Cerutti +36 more
201538 citations
Semantic Scholar
pH Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4
Jason M. Swails, Yilin Meng, F. Walker, M. Marti +2 more
2009Journal of Physical Chemistry B37 citations Open access
Semantic Scholar
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
N. Moriarty, Paweł A. Janowski, Jason M. Swails, Hai Nguyen +3 more
2019bioRxiv33 citations Open access
Semantic Scholar
A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease.
Jinfeng Liu, Jason M. Swails, J. Zhang, Xiao He +1 more
2018Journal of the American Chemical Society20 citations Open access
Semantic Scholar
PYTRAJ v1.0.0.dev1: Interactive data analysis for molecular dynamics simulations
Hai Nguyen, Jason M. Swails, D. Roe, D. Case
201614 citations
Semantic Scholar
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
M. Shirts, Christoph Klein, Jason M. Swails, Jian Yin +4 more
2017Journal of Computer-Aided Molecular Design13 citations Open access
Semantic Scholar
Synthesis and characterization of κ-2-bis-N-heterocyclic carbene rhodium(I) catalysts: Application in enantioselective arylboronic acid addition to cyclohex-2-enones
Matthew S. Jeletic, Roxy J. Lowry, Jason M. Swails, I. Ghiviriga +1 more
201113 citations
Semantic Scholar
Improved Accuracy for Constant pH-REMD Simulations through Modification of Carboxylate Effective Radii.
Andrew Yeager, Jason M. Swails, Bill R. Miller
2017Journal of Chemical Theory and Computation8 citations Open access
Semantic Scholar
Improved chemistry restraints for crystallographic refinement by integrating Amber molecular mechanics in Phenix
D. Case, Paweł A. Janowski, N. Moriarty, Jason M. Swails +1 more
2018Acta Crystallographica Section A: Foundations and Advances4 citations Open access
Semantic Scholar
Free Energy Simulations of Complex Biological Systems at Constant pH
Jason M. Swails
20133 citations
Semantic Scholar
Multi-Modal and Multi-Task Transformer for Small Molecule Drug Discovery
Sai Krishna, Sirumalla, Davide Farina, Zhuoran Qiao +12 more
3 citations
Semantic Scholar
MDTraj 1.4.2
R. McGibbon, Christian R. Schwantes, Jason M. Swails, T. Lane +6 more
20150 citations
Semantic Scholar
Mixed Quantum-Classical Calculations in Biological Systems
G. Seabra, Jason M. Swails, A. Roitberg
20090 citations
Semantic Scholar
Interpretation of pH − Activity Pro ﬁ les for Acid − Base Catalysis from Molecular Simulations
Thakshila Dissanayake, Jason M. Swails, M. Harris, A. Roitberg +3 more
0 citations
Semantic Scholar

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