Jessica Swanson - Publications

Affiliations: 
Molecular & Human Genetics Baylor College of Medicine, Houston, TX 

44 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
2021 Aydin F, Durumeric AEP, da Hora GCA, Nguyen JDM, Oh MI, Swanson JMJ. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. The Journal of Chemical Physics. 155: 045101. PMID 34340389 DOI: 10.1063/5.0055489  0.01
2021 Kim S, Oh MI, Swanson JMJ. Stressed Lipid Droplets: How Neutral Lipids Relieve Surface Tension and Membrane Expansion Drives Protein Association. The Journal of Physical Chemistry. B. PMID 34014091 DOI: 10.1021/acs.jpcb.1c01795  0.01
2020 Turgeon Z, Sierocinski T, Brimacombe CA, Jin Y, Goldhawke B, Swanson JM, Husnik JI, Dahabieh MS. Creation and Characterization of Industrially Applicable Lager Yeast Hybrids with a Unique Genomic Architecture. Applied and Environmental Microbiology. PMID 33188002 DOI: 10.1128/AEM.02434-20  0.01
2020 Kim S, Swanson JMJ. The Surface and Hydration Properties of Lipid Droplets. Biophysical Journal. PMID 33120015 DOI: 10.1016/j.bpj.2020.10.001  0.04
2020 Olarte MJ, Kim S, Sharp ME, Swanson JMJ, Farese RV, Walther TC. Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting. Developmental Cell. PMID 32730754 DOI: 10.1016/J.Devcel.2020.07.001  0.01
2020 Hanson E, Swanson J, Arenkiel BR. GABAergic Input From the Basal Forebrain Promotes the Survival of Adult-Born Neurons in the Mouse Olfactory Bulb. Frontiers in Neural Circuits. 14: 17. PMID 32390805 DOI: 10.3389/Fncir.2020.00017  0.84
2019 Patel JM, Swanson J, Arenkiel BR. Optogenetic Food Odor Avoidance Assay. Bio-Protocol. 9: e3406. PMID 33654907 DOI: 10.21769/BioProtoc.3406  0.84
2019 Wang Z, Swanson JMJ, Voth GA. Local conformational dynamics regulating transport properties of a Cl /H antiporter. Journal of Computational Chemistry. PMID 31633205 DOI: 10.1002/Jcc.26093  0.01
2019 Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. Journal of the American Chemical Society. PMID 31382734 DOI: 10.1021/Jacs.9B04387  0.01
2019 Watkins LC, Liang R, Swanson JMJ, DeGrado WF, Voth GA. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. Journal of the American Chemical Society. PMID 31264413 DOI: 10.1021/Jacs.9B05136  0.01
2019 Aydin F, Sun R, Swanson JMJ. Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations. Biophysical Journal. PMID 31174850 DOI: 10.1016/J.Bpj.2019.05.012  0.01
2019 Patel JM, Swanson J, Ung K, Herman A, Hanson E, Ortiz-Guzman J, Selever J, Tong Q, Arenkiel BR. Sensory perception drives food avoidance through excitatory basal forebrain circuits. Elife. 8. PMID 31074744 DOI: 10.7554/Elife.44548  0.84
2019 Patel JM, Swanson J, Ung K, Herman A, Hanson E, Ortiz-Guzman J, Selever J, Tong Q, Arenkiel BR. Author response: Sensory perception drives food avoidance through excitatory basal forebrain circuits Elife. DOI: 10.7554/Elife.44548.019  0.84
2018 Wang Z, Swanson JMJ, Voth GA. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux. Journal of the American Chemical Society. PMID 30421606 DOI: 10.1021/Jacs.8B07614  0.01
2018 Sun R, Han Y, Swanson JMJ, Tan JS, Rose JP, Voth GA. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. The Journal of Chemical Physics. 149: 072310. PMID 30134730 DOI: 10.1063/1.5027004  0.01
2018 Liu G, Patel JM, Tepe B, McClard CK, Swanson J, Quast KB, Arenkiel BR. An Objective and Reproducible Test of Olfactory Learning and Discrimination in Mice. Journal of Visualized Experiments : Jove. PMID 29630042 DOI: 10.3791/57142  0.84
2018 López CA, Unkefer CJ, Swanson BI, Swanson JMJ, Gnanakaran S. Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans. Plos Computational Biology. 14: e1005972. PMID 29401455 DOI: 10.1371/Journal.Pcbi.1005972  0.01
2018 Nelson JG, Peng Y, Silverstein DW, Swanson JMJ. Correction to Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation. Journal of Chemical Theory and Computation. PMID 29392951 DOI: 10.1021/Acs.Jctc.8B00044  0.04
2018 Mayes HB, Lee S, White AD, Voth GA, Swanson JMJ. Multiscale kinetic modeling reveals ensemble of Cl-/H+ exchange pathways in ClC-ec1 antiporter. Journal of the American Chemical Society. PMID 29332400 DOI: 10.1021/Jacs.7B11463  0.04
2017 Parker JL, Li C, Brinth A, Wang Z, Vogeley L, Solcan N, Ledderboge-Vucinic G, Swanson JMJ, Caffrey M, Voth GA, Newstead S. Proton movement and coupling in the POT family of peptide transporters. Proceedings of the National Academy of Sciences of the United States of America. 114: 13182-13187. PMID 29180426 DOI: 10.1073/Pnas.1710727114  0.01
2017 Hanson E, Swanson J, Arenkiel BR. Sensory experience shapes the integration of adult-born neurons into the olfactory bulb. Journal of Nature and Science. 3. PMID 28884145  0.84
2017 Liu G, McClard CK, Tepe B, Swanson J, Pekarek B, Panneerselvam S, Arenkiel BR. Olfactory Cued Learning Paradigm. Bio-Protocol. 7. PMID 28752111 DOI: 10.21769/BioProtoc.2251  0.84
2017 Liang R, Swanson JMJ, Wikström M, Voth GA. Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. PMID 28536198 DOI: 10.1073/Pnas.1703654114  0.01
2016 Liang R, Swanson JM, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid activation mechanism of the influenza A M2 proton channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791184 DOI: 10.1073/Pnas.1615471113  0.01
2016 Lee S, Mayes HB, Swanson JM, Voth GA. The Origin of Coupled Chloride and Proton Transport in a Cl-/H+ Antiporter. Journal of the American Chemical Society. PMID 27783900 DOI: 10.1021/Jacs.6B06683  0.01
2016 Liang R, Swanson JM, Peng Y, Wikström M, Voth GA. Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. PMID 27339133 DOI: 10.1073/Pnas.1601982113  0.08
2016 Taraphder S, Maupin CM, Swanson JM, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. The Journal of Physical Chemistry. B. PMID 27063577 DOI: 10.1021/Acs.Jpcb.6B02166  0.08
2016 Lee S, Swanson JM, Voth GA. Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophysical Journal. 110: 1334-1345. PMID 27028643 DOI: 10.1016/J.Bpj.2016.02.014  0.08
2016 Lee S, Liang R, Voth GA, Swanson JM. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. Journal of Chemical Theory and Computation. PMID 26734942 DOI: 10.1021/Acs.Jctc.5B01109  0.08
2014 Peng Y, Swanson JM, Kang SG, Zhou R, Voth GA. Hydrated Excess Protons Can Create Their Own Water Wires. The Journal of Physical Chemistry. B. PMID 25369445 DOI: 10.1021/Jp5095118  0.08
2014 Liang R, Swanson JM, Voth GA. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. Journal of Chemical Theory and Computation. 10: 451-462. PMID 25104919 DOI: 10.1021/Ct400832R  0.08
2014 Nelson JG, Peng Y, Silverstein DW, Swanson JM. Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation. Journal of Chemical Theory and Computation. 10: 2729-2737. PMID 25061442 DOI: 10.1021/Ct500250F  0.08
2014 Liang R, Li H, Swanson JM, Voth GA. Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel. Proceedings of the National Academy of Sciences of the United States of America. 111: 9396-401. PMID 24979779 DOI: 10.1073/Pnas.1401997111  0.08
2011 Izvekov S, Swanson JM. Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations. The Journal of Chemical Physics. 134: 194109. PMID 21599046 DOI: 10.1063/1.3591374  0.01
2010 Lee HJ, Svahn E, Swanson JM, Lepp H, Voth GA, Brzezinski P, Gennis RB. Intricate role of water in proton transport through cytochrome c oxidase. Journal of the American Chemical Society. 132: 16225-39. PMID 20964330 DOI: 10.1021/Ja107244G  0.08
2009 Swanson JM, Simons J. Role of charge transfer in the structure and dynamics of the hydrated proton. The Journal of Physical Chemistry. B. 113: 5149-61. PMID 19309128 DOI: 10.1021/Jp810652V  0.01
2008 Izvekov S, Swanson JM, Voth GA. Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials. The Journal of Physical Chemistry. B. 112: 4711-24. PMID 18366209 DOI: 10.1021/Jp710339N  0.01
2007 Swanson JM, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation. 3: 170-83. PMID 26627162 DOI: 10.1021/ct600216k  0.08
2007 Swanson JM, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. The Journal of Physical Chemistry. B. 111: 4300-14. PMID 17429993 DOI: 10.1021/Jp070104X  0.08
2005 Swanson JM, Adcock SA, McCammon JA. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. Journal of Chemical Theory and Computation. 1: 484-93. PMID 26641515 DOI: 10.1021/Ct049834O  0.01
2005 Swanson JM, Mongan J, McCammon JA. Limitations of atom-centered dielectric functions in implicit solvent models. The Journal of Physical Chemistry. B. 109: 14769-72. PMID 16852866 DOI: 10.1021/Jp052883S  0.01
2005 Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophysical Journal. 89: L25-7. PMID 16100267 DOI: 10.1529/Biophysj.105.069336  0.01
2004 Swanson JM, Henchman RH, McCammon JA. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophysical Journal. 86: 67-74. PMID 14695250 DOI: 10.1016/S0006-3495(04)74084-9  0.04
2003 Zheng X, Medvedev DM, Swanson J, Stuchebrukhov AA. Computer simulation of water in cytochrome c oxidase Biochimica Et Biophysica Acta - Bioenergetics. 1557: 99-107. PMID 12615353 DOI: 10.1016/S0005-2728(03)00002-1  0.08
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