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Jason M. Swails, Ph.D. - Publications

Affiliations: 
2013 University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Physical Chemistry, Theory Physics, Molecular Chemistry
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19 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, ... ... Swails J, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153  0.525
2020 Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallographica. Section D, Structural Biology. 76: 51-62. PMID 31909743 DOI: 10.1107/S2059798319015134  0.318
2018 Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. Journal of the American Chemical Society. PMID 29308643 DOI: 10.1021/Jacs.7B08569  0.608
2017 Yeager AV, Swails JM, Miller Iii BR. Improved accuracy for constant pH-REMD simulations through modification of carboxylate effective radii. Journal of Chemical Theory and Computation. PMID 28910090 DOI: 10.1021/Acs.Jctc.7B00638  0.467
2017 Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659. PMID 28746339 DOI: 10.1371/Journal.Pcbi.1005659  0.339
2016 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/S10822-016-9977-1  0.477
2016 Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/Acs.Jpcb.6B06414  0.393
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  0.368
2015 McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal. 109: 1528-32. PMID 26488642 DOI: 10.1016/J.Bpj.2015.08.015  0.354
2015 Swails J, Zhu T, He X, Case DA. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Journal of Biomolecular Nmr. 63: 125-39. PMID 26232926 DOI: 10.1007/S10858-015-9970-3  0.37
2015 Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry. 54: 1307-13. PMID 25615525 DOI: 10.1021/Bi5012833  0.593
2014 Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. Journal of Chemical Theory and Computation. 10: 1341-1352. PMID 24803862 DOI: 10.1021/Ct401042B  0.63
2014 Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of Chemical Theory and Computation. 10: 492-499. PMID 24453949 DOI: 10.1021/Ct400862K  0.547
2013 Cui G, Swails JM, Manas ES. SPAM: A Simple Approach for Profiling Bound Water Molecules. Journal of Chemical Theory and Computation. 9: 5539-49. PMID 26592287 DOI: 10.1021/Ct400711G  0.345
2012 Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. Journal of Chemical Theory and Computation. 8: 3314-3321. PMID 26605738 DOI: 10.1021/Ct300418H  0.682
2012 Swails JM, Roitberg AE. Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 8: 4393-4404. PMID 26605601 DOI: 10.1021/Ct300512H  0.622
2012 Swails JM, Roitberg AE. Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics Journal of Chemical Theory and Computation. 8: 4393-4404. DOI: 10.1021/ct300512h  0.577
2012 Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: An efficient program for end-state free energy calculations Journal of Chemical Theory and Computation. 8: 3314-3321. DOI: 10.1021/ct300418h  0.666
2009 Swails JM, Meng Y, Walker FA, Marti MA, Estrin DA, Roitberg AE. pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4. The Journal of Physical Chemistry. B. 113: 1192-201. PMID 19159340 DOI: 10.1021/Jp806906X  0.65
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