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J

Jason Swails

iambic therapeutics, 5627 oberlin drive, suite 120, san diego, california 92121, united states

21H-index
54Paper Count
1.8WCitation Count
Published Papers 13
Publication Date
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Recent Developments in Amber Biomolecular Simulations
errJournal of Chemical Information and Modeling
IF5.3
err2025-07-29
err0
errOAAI
errDavid A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambaşu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; Zhen Li; Charles Lin; Jian Liu; Yinglong Miao; Romelia Salomon-Ferrrer; Jana Shen; Ryan Snyder; Jason Swails; Ross C. Walker; Jinan Wang; Xiongwu Wu; Jinzhe Zeng; Thomas E. Cheatham III; Daniel R. Roe; Adrian Roitberg; Carlos Simmerling; Darrin M. York; Maria C. Nagan; Kenneth M. Merz Jr.
errShare
errSave
The AmberTools
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-10-08
err474
errOAAI
errCase, David A.; Aktulga, Hasan Metin; Belfon, Kellon; Cerutti, David S.; Cisneros, G. Andres; Cruzeiro, Vinicus Wilian D.; Forouzesh, Negin; Giese, Timothy J.; Gotz, Andreas W.; Gohlke, Holger; Izadi, Saeed; Kasavajhala, Koushik; Kaymak, Mehmet C.; King, Edward; Kurtzman, Tom; Lee, Tai-Sung; Li, Pengfei; Liu, Jian; Luchko, Tyler; Luo, Ray; Manathunga, Madushanka; Machado, Matias R.; Nguyen, Hai Minh; O'Hearn, Kurt A.; Onufriev, Alexey V.; Pan, Feng; Pantano, Sergio; Qi, Ruxi; Rahnamoun, Ali; Risheh, Ali; Schott-Verdugo, Stephan; Shajan, Akhil; Swails, Jason; Wang, Junmei; Wei, Haixin; Wu, Xiongwu; Wu, Yongxian; Zhang, Shi; Zhao, Shiji; Zhu, Qiang; Cheatham, I. I. I. Thomas E.; Roe, Daniel R.; Roitberg, Adrian; Simmerling, Carlos; York, Darrin M.; Nagan, Maria C.; Merz, Jr Kenneth M.
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errSave
A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2018-01-27
err22
PREAI
errLiu, Jinfeng; Swails, Jason; Zhang, John Z. H.; He, Xiao; Roitberg, Adrian E.
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errSave
Improved Accuracy for Constant pH-REMD Simulations through Modification of Carboxylate Effective Radii
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2017-09-29
err7
PREAI
errYeager, Andrew V.; Swails, Jason M.; Miller, Bill R., III
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errSave
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset (vol 31, pg 147, 2017)
errJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
IF3.1
err2017-07-27
err3
errOAAI
errShirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.
errShare
errSave
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
errJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
IF3.1
err2016-10-27
err239
errOAAI
errShirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.
errShare
errSave
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2015-12-03
err1.7K
errOAAI
errLee, 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., III; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Im, Wonpil
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errSave
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
errBIOPHYSICAL JOURNAL
IF3.1
err2015-10-01
err1.6K
errOAAI
errMcGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernandez, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.
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errSave
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2014-02-25
err230
errOAAI
errSwails, Jason M.; York, Darrin M.; Roitberg, Adrian E.
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errSave
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2013-11-22
err128
errOAAI
errBergonzo, Christina; Henriksen, Niel M.; Roe, Daniel R.; Swails, Jason M.; Roitberg, Adrian E.; Cheatham, Thomas E., III
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errSave
SPAM: A Simple Approach for Profiling Bound Water Molecules
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2013-11-12
err44
PREAI
errCui, Guanglei; Swails, Jason M.; Manas, Eric S.
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errSave
Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2012-09-14
err100
PREAI
errSwails, Jason M.; Roitberg, Adrian E.
errShare
errSave
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2012-08-16
err3.2K
PREAI
errMiller, Bill R., III; McGee, T. Dwight, Jr.; Swails, Jason M.; Homeyer, Nadine; Gohlke, Holger; Roitberg, Adrian E.
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errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
V
Vijay S. Pande
H-index: 110 · Papers: 494
A
Alexander D. MacKerell
H-index: 107 · Papers: 766
D
David A. Case
H-index: 107 · Papers: 518
C
Charles L. Brooks
H-index: 104 · Papers: 675
M
Michael K. Gilson
H-index: 83 · Papers: 411
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