USF Home
>
College of Arts and Sciences
> Computational Biophysics
Home
Research
Team
Publications
Software (External @ SimTK)
J.M. Delgado and S. Varma, ATP-ion complexation and lithium's bioactive form.
In preparation.
J.M. Delgado, G. Schillaci and S. Varma, Phosphate and protein phosphorylation parameters for AMOEBA polarizable force field with high field corrections.
In preparation.
G. W. Dayhoff II and S. Varma, Machine learning velocities to propagate molecular dynamics simulations.
In preparation.
J. G. Guergues, J. Koomen, J. Wohlfahrt, J. Krieger, S. Varma and S. M. Stevens Jr., A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis. Proteomics, 2024.
In press
P.S. Higbee
e
, G. W. Dayhoff II
e
, A. Anbanandam, S. Varma and G. Daughdrill, Structural adaptation of p53 to secondary binding sites on MDM2 and MDMX. J Mol. Biol. 436: 168626, 2024.
(e: equal contribution)
View
J.M. Delgado, P. Nagy and S. Varma, Polarizable AMOEBA model for simulating Mg
2+
·Protein·Nucleotide Complexes. J. Chem. Info. Model. 64: 378-392, 2024.
View
R.R. Cueny, S. Varma, K.H. Schmidt and J.L. Keck, Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants. PLOS One. 18: e0281524, 2023.
View
N. Rogic, S.J. Charbonnier, F.Garin1, G.W. Dayhoff II, E. Gagliano, M. Rodgers, C.B. Connor, S. Varma and D. Shean, Characterizing and Mapping Volcanic Flow Deposits on Mount St. Helens via Dual-band SAR Imagery. Remote Sensing. 5: 2791, 2023.
View
J.M. Delgado, V. Wineman-Fisher, S.A. Pandit and S. Varma, Inclusion of high-field target data in AMOEBA’s calibration improves predictions of protein-ion interactions. J. Chem. Info. Model, 62: 4713–4726, 2022.
View
M. Saunders, V. Wineman-Fisher, E. Jakobsson, S. Varma and S.A. Pandit, High-dimensional parameter search method to determine force field mixing terms in molecular simulations. Langmuir, 38: 2840–2851, 2022.
View
S. Varma, J.P.R.O. Orgel and J.D. Schieber, Contrasting local and macroscopic effects of collagen hydroxylation. Int. J. Mol. Sci. 22: 9068, 2021.
View
J.M. Delgado, N. Duro, D.M. Rogers, A. Tkatchenko, S.A. Pandit and S. Varma, Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor. Proteins 89: 1134-1144, 2021.
View
S. Rahman, V. Wineman-Fisher, P. Nagy, Y. Al-Hamdani, A. Tkatchenko and S. Varma, Methyl-induced polarization destabilizes non-covalent interactions of N-methylated lysines. Chem. Euro. J. 27: 11005-11014, 2021.
View
C.L. Kriss, N. Duro, O.W. Nadeau, J. Guergues, O. Chavez-Chiang, A.E. Culver-Cochran, D. Chaput, S. Varma and S.M. Stevens Jr., Site‐specific identification and validation of hepatic histone nitration in vivo: Implications for alcohol‐induced liver injury. J Mass Spectrom. 56: e4713, 2021
View
S. Rahman, V. Wineman-Fisher, Y. Al-Hamdani, A. Tkatchenko and S. Varma, Predictive QM/MM modeling of modulations in protein-protein binding by lysine methylation. J Mol. Biol. 433: 166745, 2021
View
V. Wineman-Fisher, J.A. Melendez, P. Nagy, E. Jakobsson, S.A. Pandit and S. Varma, Transferable interactions of Li
+
and Mg
2+
ions in polarizable models. J. Chem. Phys. 153: 104113, 2020.
View
V. Wineman-Fisher, Y. Al-Hamdani, P. Nagy, A. Tkatchenko and S. Varma, Improved description of ligand polarization enhances transferability of ion-ligand interactions. J. Chem. Phys. 153:094115, 2020.
View
J. Kruczek, S.W. Chiu, S. Varma, E. Jakobsson, S.A. Pandit, Interactions of Monovalent and Divalent Cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. Langmuir, 35: 10522–10532, 2019.
View
Dedicated to Dr. Chiu: Mentor, friend and a great scientist -- thank you for teaching us the meaning of rigor!
N. Duro, and S. Varma, Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase. Structure. 27: 1-11, 2019.
View
V. Wineman-Fisher, Y. Al-Hamdani, I. Addou, A. Tkatchenko and S. Varma, Ion-hydroxyl interactions: From high-level quantum benchmarks to transferable polarizable force fields. J Chem. Theory and Comput. 15: 2444−2453, 2019.
View
M. Saunders, M. Steele, W. Lavigne, S. Varma and S.A. Pandit, Interactions of salt with ether- and ester-linked phospholipid bilayers. BBA biomembranes. 1861: 907-915, 2019.
View
M. Botlani, A. Siddiqui and S. Varma, Machine learning approaches to evaluate correlation patterns in allosteric signaling: a case study of the PDZ2 domain. J Chem. Phys. 148. 2018.
Featured Article
View
Press Release
P. Dutta, A. Siddiqui, M. Botlani and S. Varma, Stimulation of Nipah Fusion: Small Intradomain Changes Trigger Extensive Interdomain Rearrangements. Biophys. J. 111: 1621–1630, 2016.
View
N. Duro
e
, M. Gjika
e
, A. Siddiqui, H.L. Scott and S. Varma, POPC bilayers supported on nanoporous substrates: specific effects of silica-type surface hydroxylation and charge density. Langmuir. 32: 6766–6774, 2016.
View
(e: equal contribution)
S. Varma, J.P.R.O. Orgel and J.D. Schieber, Nanomechanics of Type I collagen. Biophys. J. 111: 50-56, 2016.
View
P.K. Bahia, T.A. Parks, K.R. Stanford, D.A. Mitchell, S. Varma, S.M. Stevens Jr. amd T.E. Taylor-Clark, The exceptionally high reactivity of Cys 621 is critical for electrophilic activation of the sensory nerve ion channel TRPA1. J Gen. Physiol. 147: 451-465, 2016.
View
D. Martin, P. Dutta, S. Mahajan, S. Varma and S. M. Stevens Jr., Structural and activity characterization of human PHPT1 after oxidative modification. Scientific Reports. 6:23658, 2016.
View
P.M. Dutov, O. Antipova, S. Varma, J.P.R.O. Orgel and J.D. Schieber, Measurement of elastic modulus of collagen type I single fiber. PLoS ONE. 11: e0145711, 2016.
View
S. Varma, M. Botlani, J. Hammond, H.L. Scott, J.P.R.O Orgel and J.D. Schieber, Effect of intrinsic and extrinsic factors on the simulated D-band length of Type I collagen. Proteins. 83: 1800–1812, 2015.
View
C. N. Krute, R. K. Carroll, F. E. Rivera, A. Weiss, R. M. Young, M. Botlani, S. Varma, B. J. Baker, L. N. Shaw. The Disruption of Prenylation Leads to Pleiotropic Rearrangements in Cellular Behavior and Virulence in Staphylococcus aureus. Molecular Microbiology. 95:819-32, 2015.
View
P. Dutta, M. Botlani and S. Varma, Water dynamics at protein-protein interfaces: A molecular dynamics study of virus-host receptor complexes. J Phys. Chem. B. 118: 14795-14807, 2014.
View
S. Varma, M. Botlani and R.E. Leighty, Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning. Proteins. 82: 3241-3254, 2014.
View
M. Rossi, A. Tkatchenko, S.B. Rempe and S. Varma, Role of methyl-induced polarization in ion binding. Proc. Natl. Acad. Sci. U.S.A. 110: 12978-12983, 2013.
View
D. Sabo, D. Jiao, S. Varma, L.R. Pratt and S.B. Rempe, Case study of Rb
+
(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule. Ann. Rep. Prog. Chem. Sect. C. 109: 266-278, 2013.
View
R.E. Leighty and S. Varma, Quantifying changes in intrinsic molecular motion using support vector machines. J Chem. Theory and Comput. 9: 868–875, 2013.
View
S. Varma, M. Teng and H. Larry Scott, Non-intercalating nanosubstrates create asymmetry between bilayer leaflets. Langmuir 28: 2842-2848, 2012.
View
S. Varma, D.M. Rogers, L.R. Pratt and S.B. Rempe, Perspectives on: Ion selectivity Design principles for K
+
selectivity in membrane transport. J Gen. Physiol. 137: 479-488, 2011.
Invited Review
View
S. Varma and S.B. Rempe, Multi-body effects in ion binding and selectivity. Biophys. J, 99: 3394-3401, 2010.
View
D. Asthagiri, P.D. Dixit, S. Merchant, M.E. Paulaitis, L.R. Pratt, S.B. Rempe and S. Varma, Ion selectivity from local configuration of ligands in solutions and ion channels. Chem. Phys. Letts. 485: 1-7, 2010
Cover Article
View
S. Varma and S.B. Rempe, Structural transitions in ion coordination driven by changes in competition for ligand binding. J Amer. Chem. Soc. 130, 15405-15419, 2008.
View
D. Sabo, S. Varma, M. Martin and S.B. Rempe, Studies of the thermodynamic properties of hydrogen gas in bulk water. J Phys. Chem. B.112, 867-876, 2008.
View
S. Varma, D. Sabo and S.B. Rempe, K
+
/Na
+
selectivity in K-channels and Valinomycin: Over-coordination Vs Cavity-size constraints. J Mol. Biol. 376, 13-22, 2008.
View
T. Whitfield, S. Varma, E. Harder, G. Lamoureux, S.B. Rempe and B. Roux, Theoretical Study of Aqueous solvation of K
+
: Comparison of ab initio, polarizable and fixed charge models. J Chem. Theo. Comput. 3, 2068-2082, 2007.
View
S. Varma and S.B. Rempe, Tuning ion coordination architectures to enable selective partitioning. Biophys J. 93, 1093-1099, 2007.
New and Notable article
View
S. Varma and E. Jakobsson, The cPLA2 C2α Domain in Solution: Structure and Dynamics of its Ca
2+
-activated and Cation-free States. Biophys. J., 92, 966-976, 2007.
View
S. Varma and S.B. Rempe, Coordination numbers of alkali metal ions in aqueous solutions. J Biophys. Chem., 124, 192-199, 2006. Invited Review
View
S. Varma, S. W. Chiu and E. Jakobsson, The influence of amino acid protonation states on molecular dynamics simulations of a bacterial porin OmpF. Biophys. J., 90, 112-123, 2006.
View
N.J. Malmberg, S. Varma, E. Jakobsson and J.J. Falke, Ca
2+
Activation of the cPLA2 C2 Domain: Ordered Binding of Two Ca
2+
Ions with Positive Cooperativity. Biochemistry, 43, 16320-16328, 2004.
View
S. Natarajan, S. Varma, Y. Tang, S. Parker, J. Mashl and E. Jakobsson, Toward an Integrated Computational Environment for Multiscale Computational Design of Nanoscale Ion Channel Semiconductors, ICCN, 1, 147-150, 2004.
View
S. Varma and E. Jakobsson, Ionization states of residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions between Residues. Biophys. J, 86, 690-704, 2004.
View
T. van der Straaten., S. Varma, C-W Chiu, Y. Tang, N.R. Aluru, R. Eisenberg, U. Ravaioli and E. Jakobsson, Combining Computational Chemistry and Computational Electronics to Understand Protein Ion Channels. ICCN, 2, 60-63, 2002.
View