| Year |
Citation |
Score |
| 2022 |
Saunders M, Wineman-Fisher V, Jakobsson E, Varma S, Pandit SA. High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 35192365 DOI: 10.1021/acs.langmuir.1c03105 |
0.523 |
|
| 2020 |
Wineman-Fisher V, Delgado JM, Nagy PR, Jakobsson E, Pandit SA, Varma S. Transferable interactions of Li and Mg ions in polarizable models. The Journal of Chemical Physics. 153: 104113. PMID 32933310 DOI: 10.1063/5.0022060 |
0.567 |
|
| 2020 |
Wineman-Fisher V, Al-Hamdani Y, Nagy PR, Tkatchenko A, Varma S. Improved description of ligand polarization enhances transferability of ion-ligand interactions. The Journal of Chemical Physics. 153: 094115. PMID 32891085 DOI: 10.1063/5.0022058 |
0.374 |
|
| 2019 |
Duro N, Varma S. Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase. Structure (London, England : 1993). PMID 31402221 DOI: 10.1016/J.Str.2019.07.005 |
0.33 |
|
| 2019 |
Kruczek J, Chiu SW, Varma S, Jakobsson E, Pandit S. Interactions of Mono and Di-valent cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 31337218 DOI: 10.1021/Acs.Langmuir.9B01275 |
0.557 |
|
| 2019 |
Wineman-Fisher V, Al-Hamdani Y, Addou I, Tkatchenko A, Varma S. Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields. Journal of Chemical Theory and Computation. PMID 30830778 DOI: 10.1021/Acs.Jctc.8B01198 |
0.334 |
|
| 2019 |
Saunders M, Steele M, Lavigne W, Varma S, Pandit SA. Interaction of salt with ether- and ester-linked phospholipid bilayers. Biochimica Et Biophysica Acta. Biomembranes. PMID 30742804 DOI: 10.1016/J.Bbamem.2019.01.016 |
0.348 |
|
| 2018 |
Botlani M, Siddiqui A, Varma S. Machine learning approaches to evaluate correlation patterns in allosteric signaling: A case study of the PDZ2 domain. The Journal of Chemical Physics. 148: 241726. PMID 29960337 DOI: 10.1063/1.5022469 |
0.322 |
|
| 2016 |
Bahia PK, Parks TA, Stanford KR, Mitchell DA, Varma S, Stevens SM, Taylor-Clark TE. The exceptionally high reactivity of Cys 621 is critical for electrophilic activation of the sensory nerve ion channel TRPA1. The Journal of General Physiology. 147: 451-65. PMID 27241698 DOI: 10.1085/Jgp.201611581 |
0.324 |
|
| 2016 |
Martin DR, Dutta P, Mahajan S, Varma S, Stevens SM. Structural and activity characterization of human PHPT1 after oxidative modification. Scientific Reports. 6: 23658. PMID 27034094 DOI: 10.1038/Srep23658 |
0.304 |
|
| 2016 |
Duro ND, Dutta P, Varma S. Sialic Acid Induced Conformational Ensemble Shifts in the Hemagglutinin-Neuraminidase Protein of the Newcastle Disease Virus Biophysical Journal. 110: 52. DOI: 10.1016/J.Bpj.2015.11.348 |
0.307 |
|
| 2015 |
Duro ND, Gjika M, Scott L, Varma S. Structural and Dynamical Properties of POPC Bilayers Supported on Nanoporous Substrates Biophysical Journal. 108: 77a-78a. DOI: 10.1016/J.Bpj.2014.11.458 |
0.305 |
|
| 2015 |
Varma S, Dutta P, Botlani M. Allosteric Regulation of Nipah Virus Entry into Host Cells Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1989 |
0.321 |
|
| 2014 |
Dutta P, Botlani M, Varma S. Water Dynamics at Protein-Protein Interfaces: Molecular Dynamics Study of Virus-Host Receptor Complexes. The Journal of Physical Chemistry. B. PMID 25420132 DOI: 10.1016/J.Bpj.2013.11.2695 |
0.306 |
|
| 2014 |
Sabo D, Jiao D, Varma S, Pratt L, Rempe S. Density Functional Studies of Rubidium Hydration to Probe the Analogy Between Rb+ and K+ in K Channels Biophysical Journal. 106: 540a. DOI: 10.1016/J.Bpj.2013.11.3012 |
0.372 |
|
| 2013 |
Leighty RE, Varma S. Quantifying Changes in Intrinsic Molecular Motion Using Support Vector Machines. Journal of Chemical Theory and Computation. 9: 868-75. PMID 26588730 DOI: 10.1021/Ct300694E |
0.317 |
|
| 2013 |
Rossi M, Tkatchenko A, Rempe SB, Varma S. Role of methyl-induced polarization in ion binding. Proceedings of the National Academy of Sciences of the United States of America. 110: 12978-83. PMID 23878238 DOI: 10.1073/Pnas.1302757110 |
0.355 |
|
| 2013 |
Leighty RE, Varma S. Quantitative Assessment of Changes in Intrinsic Molecular Motion using Support Vector Machines Biophysical Journal. 104: 504a-505a. DOI: 10.1016/J.Bpj.2012.11.2785 |
0.317 |
|
| 2011 |
Tumaneng P, Zhao G, Antipova O, Orgel JP, Varma S, Scott HL. Mechanical Properties of Type I Collagen: Insights From Molecular Dynamics Simulations Biophysical Journal. 100: 48a. DOI: 10.1016/J.Bpj.2010.12.460 |
0.303 |
|
| 2011 |
Varma S, Teng M, Scott HL. Effect of Extrinsic Constraints on Lipid Bilayers Biophysical Journal. 100: 333a. DOI: 10.1016/J.Bpj.2010.12.2021 |
0.312 |
|
| 2010 |
Asthagiri D, Dixit PD, Merchant S, Paulaitis ME, Pratt LR, Rempe SB, Varma S. Ion selectivity from local configurations of ligands in solutions and ion channels. Chemical Physics Letters. 485: 1-7. PMID 23750043 DOI: 10.1016/J.Cplett.2009.12.013 |
0.353 |
|
| 2010 |
Varma S, Rempe SB. Multibody effects in ion binding and selectivity. Biophysical Journal. 99: 3394-401. PMID 21081088 DOI: 10.1016/J.Bpj.2010.09.019 |
0.386 |
|
| 2009 |
Varma S, Rempe S. Mechanism of Ion Recognition by Over-coordination: “The Caress of the Surroundings”[1] Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.003 |
0.382 |
|
| 2008 |
Varma S, Rempe SB. Structural transitions in ion coordination driven by changes in competition for ligand binding. Journal of the American Chemical Society. 130: 15405-19. PMID 18954053 DOI: 10.1021/Ja803575Y |
0.386 |
|
| 2008 |
Varma S, Sabo D, Rempe SB. K+/Na+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints. Journal of Molecular Biology. 376: 13-22. PMID 18155244 DOI: 10.1016/J.Jmb.2007.11.059 |
0.34 |
|
| 2007 |
Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation. 3: 2068-2082. PMID 21785577 DOI: 10.1021/Ct700172B |
0.338 |
|
| 2007 |
Varma S, Rempe SB. Tuning ion coordination architectures to enable selective partitioning. Biophysical Journal. 93: 1093-9. PMID 17513348 DOI: 10.1529/Biophysj.107.107482 |
0.363 |
|
| 2007 |
Varma S, Jakobsson E. The cPLA2 C2alpha domain in solution: structure and dynamics of its Ca2+-activated and cation-free states. Biophysical Journal. 92: 966-76. PMID 17085504 DOI: 10.1529/Biophysj.106.091850 |
0.552 |
|
| 2006 |
Varma S, Rempe SB. Coordination numbers of alkali metal ions in aqueous solutions. Biophysical Chemistry. 124: 192-9. PMID 16875774 DOI: 10.1016/J.Bpc.2006.07.002 |
0.401 |
|
| 2006 |
Varma S, Chiu SW, Jakobsson E. The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF. Biophysical Journal. 90: 112-23. PMID 16183883 DOI: 10.1529/Biophysj.105.059329 |
0.537 |
|
| 2004 |
Malmberg NJ, Varma S, Jakobsson E, Falke JJ. Ca2+ activation of the cPLA2 C2 domain: ordered binding of two Ca2+ ions with positive cooperativity. Biochemistry. 43: 16320-8. PMID 15610026 DOI: 10.1021/Bi0482405 |
0.54 |
|
| 2004 |
Varma S, Jakobsson E. Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. Biophysical Journal. 86: 690-704. PMID 14747308 DOI: 10.1016/S0006-3495(04)74148-X |
0.548 |
|
| 2004 |
Natarajan S, Varma S, Tang Y, Parker S, Mashl J, Jakobsson E. Toward an integrated computational environment for multiscale computational design of nanoscale Ion Channel semiconductors 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 147-150. |
0.633 |
|
| 2002 |
Van Der Straaten T, Varma S, Chiu SW, Tang J, Aluru N, Eisenberg R, Ravaioli U, Jakobsson E. Combining computational chemistry and computational electronics to understand protein ion channels 2002 International Conference On Computational Nanoscience and Nanotechnology - Iccn 2002. 60-63. |
0.51 |
|
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