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Software (External @ SimTK)

Molecular mechanics (MM) and quantum mechanics (QM) simulations are fast becoming powerful alternatives to wet lab experiments for studying the structure, dynamics and activity regulation of biomolucules. Our primary goals are to further enhance their capabilities for treating systems that function through increasingly more complex interactions. We have ongoing projects to (a) improve accuracy of MM force fields for treating ion-protein interactions, (b) develop hybrid QM/MM methods for predicting protein-ligand binding free energies, (c) build machine learning models for accelerating QM simulations, and (d) train machine learning models for analyzing correlated big data from simulations. We also apply QM and MM simulations in collaboration with experimental groups to address key unresolved biophysical questions in allosteric signaling, ion-protein interactions and protein-protein interactions.

Sameer Varma, PhD
Associate Professor, Department of Cell Biology, Microbiology and Molecular Biology
Affiliate Professor, Department of Physics
Office: ISA 6205
Email: svarma(AT)
Phone: 813-974-9288
Fax: 813-905-9919
Postal Address: ISA-2015, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620

Recent News
  • Sep 2022: Congrants to Julian and Vered on improving AMOEBA's performance in modeling ion-protein interactions. Our manuscript is now available in JCIM and the updated parameter set in TINKER format can be downloaded here.

  • Sep 2022: Warm welcome to Valentin and Rauf.

  • Jul 2022: Warm welcome to Koushik. Has started to 'TINKER' with polarizable force fields.

  • Apr 2022: Warm welcome to Tamara. She is starting to learn MD and wants to apply it to study IDPs.

  • Mar 2022: Warm welcome to Irene. She is starting with simulating Measles virus entry into host cells.

  • Mar 2022: Sameer Varma receives reviewer of the month award from Communications Chemistry.

  • Feb 2022: Our collaborative work toward fixing ion-lipid interactions in molecular mechanics force fields is published in Langmuir. Using high-dimensional optimization, we reduced interaction energy errors from 25 kcal/mol to 2.5 kcal/mol, which lead to predicted macroscopic properties consistent with experiment. Congratuations to the team, espeically Matthew Saunders.

  • Aug 2021: Our collaborative work on the effect of hydroxylation on collagen structure and mechanics is now published in IJMS. Consistent with experiments, our MD simulations show minor effects on macroscropic properties, but reveal extensive changes in local structure that can impact collagen's interactions with other molecules.

  • May 2021: Sanim's second paper on protein methylation is now online in Chem. Euro. J. Congrats! Here we reveal how electronic structure altered by lysine methylation affects lysine's interactions.

  • Apr 2021: Our collaborative contribution to COVID-19 researach is now published in Proteins. Here we provide a physical basis for why CoV-2's Spike binds hosts more strongly than CoV's Spike.

  • Apr 2021: Warm welcome to Nur Irfan. She is focusing on advancing our collagen research.

  • Mar 2021: Congratulations to Vered for her continued efforts to improve transferability of AMOEBA force field. Her latest work in J Chem. Phys. combines our high-field corrections with the NB-fix approach to reduce transferability errors in lithium and magnesium interactions from 10 to 1 kcal/mol.

  • Feb 2021: Our development of a new QM/MM appraoch to compute relative binding free energies is now published in J Mol. Biol.. We apply it to understand how methyllysine binding proteins recognize their preferred targets.

  • Jan 2021: Welcome to Aliya Miller and Samuel Coleman!

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