Profile Details

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Hire Dr. Sumit M.

India

USD 10 /hr

Skilled professional in MD simulations, QM/MM calculations, Docking and Free energy calculations.

Profile Summary

Technical Skills: • Molecular dynamics (MD), atomistic as well as multi-scale (MM/CG and QM/MM), simulations using NAMD, Gromacs, CHARMM packages. • Free energy calculations based on alchemical free energy perturbation (FEP) theory, umbrella sampling (US), thermodynamic integration (TI), adaptive biasing force (ABF) methods. • Ligand docking with AutoDock Vina and other web-server based docking tools. • Small molecule parameterization for CHARMM, Amber and OPLS force-fields. • Enhanced sampling methods such as replica exchange molecular dynamics (REMD). • Pure QM and hybrid QM/MM calculations using Gaussian, Turbomole, ChemShell etc packages. • Closely worked with multidisciplinary collaborators and familiar with various chemical and biophysical experimental techniques.

Subject Matter Expertise

• ★ Molecular Modeling
• ★ Quantum Chemistry
• ★ Computational Chemistry
• ☆ Chemoinformatics

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization

Work Experience

Assist. Professor

VIT University

June 2018 - Present

Education

PhD (Chemistry)

Ruhr University Bochum

August 2013 - May 2017

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

(2021). Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge . Nature methods.

(2020). Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials . Journal of Chemical Information and Modeling.

Vant, J.W., Lahey, S.-L.J., Jana, K., Shekhar, M., Sarkar, D., Munk, B.H., Kleinekathöfer, U., Mittal, S., Rowley, C., Singharoy, A.(2020). Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials . Journal of Chemical Information and Modeling. 60. (5). p. 2591-2604.

(2019). Solvent‐Enhanced Conformational Flexibility of Cyclic Tetrapeptides . ChemPhysChem.

(2018). Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers . The Journal of Physical Chemistry B.

(2018). Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein . ChemBioChem.

(2017). The Molecular Tweezer CLR01 Stabilizes a Disordered Protein–Protein Interface . Journal of the American Chemical Society.

(2017). Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01 . Journal of the American Chemical Society.

(2015). Molecular Tweezers Inhibit Islet Amyloid Polypeptide Assembly and Toxicity by a New Mechanism . ACS Chemical Biology.

BOOK CHAPTER

Vant, J.W., Sarkar, D., Gupta, C., Shekhar, M.S., Mittal, S., Singharoy, A.(2020). Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange . Methods in Molecular Biology. 2165. p. 301-315.