Computational Modelling for Emerging Drug Technologies
Multifaceted Approach for Covalent Inhibitors
Posts by Collection
research
Free Energy Estimation
Published:
SILCS is a molecular docking technique developed by Alexander D. MacKerell Jr. and group. It combines molecular dynamics and Monte Carlo techniques to calculate grid free energy of a range of chemically diverse ligands. SILCS approach results into SILCS FragMaps representative of LGFE of basic ligand types. These FragMaps can then be used for designing drugs which show maximum affinity of binding. This is an ongoing project, the details of which will soon be released on the website.
Generalization of CHARMM Molecular Force-Field to Small Molecules
Published:
A typical biomolecule like protein, lipid membrane, cholesterol has typically more than 1000 atoms. Including local environments like water and ions adds typically more than 10000 atoms to the system. Handling such large system requires very simple potential function. Additionally, we are often interested in studying interaction of small molecules with biomolecules. Atomistic force-field defines molecular potential in terms of empirical functions for bonded and non-bonded components. To ensure correct behavior of the empirical functions they are generally fitted against quantum mechanically derived target data such as dipole moment, molecular polarizability, vibrational spectra, potential energy scans. But ultimate goal of any force- field is to correctly represent bulk properties. that My research interest includes methodological advances of chemical phenomena. I want to use my expertise of computing, quantum chemistry and molecular mechanics to improve the accuracy and precision of current drug and catalyst design protocols. This involves formulation, development, implementation and application of QM mediated free energy estimation methodologies as well as ease of use of the entire computational exercise. The scope of this work involves use of a range of chemical models with increasing complexity such as molecular docking, molecular mechanics and quantum mechanics. I have worked on each of these components during my research career as PhD and Postdoc. Following is brief description of key areas which I have been worked in.
Topographical Analysis of Electron Density and Electrostatic Potential
Lone pairs: An Electrostatic Perspective
softwares
teaching
Undergraduate Tutorial Experience
Undergraduate course, IIT Kanpur, 2015
Courses:
- Basic Physical Chemistry (2013, 2014)
- Chemical Science (2015)
Workshops and Schools
Workshop, Various, 2021
Advanced Molecular Dynamics
Summer School, IISER Pune & Kathmandu University — 2021
Role: Teaching Assistant and Core Member
- Helped develop and deliver tutorials on molecular dynamics concepts and tools
- Supported students during hands-on sessions using CHARMM and OpenMM
Graduate Teaching Experience
Graduate course, University of Maryland Baltimore, Department of Pharmaceutical Sciences, 2022
Course: Advanced Quantum Chemistry
Role: Instructor
Responsibilities:
- Developed course content and assessment modules
- Delivered lectures on Schrodinger’s Equation for one- and many- electron systems
- Delivered lectures on use of Hartree-Fock, postHartree-Fock methods and DFT functionals
- Delivered lectures on Slater and Gausssian-type basis-sets
- Designed computational chemistry assignments involving Gaussian and Psi4