Mohd Athar

Background

About Mohd Athar

My field of expertise is molecular modeling of small molecule, macromolecule to polymers. Had previously lead medchem aspects of the drug-discovery projects utilizing range of computational chem techniques. I love to tinker with technology, employ new methods and software for a variety of applications. Currently, investigating RND transporters in particular AcrB and MexB/D/F/Y in regard to the transportation of the substrate along the channel using atomistic and coarse grain simulations. My Key Expertise include->Proficient in utilizing software packages such as Schrödinger Suite, Molecular Operating Environment (MOE), Discovery Studio, MGLTools, Amber, Gromacs, NAMD, Gaussian, and Cresset, along with other computational chemistry tools->Extensive experience in conducting molecular dynamics simulations, including classical MD simulations and enhanced sampling techniques like Umbrella sampling, metadynamics. Skilled in performing MMPBSA/GBSA binding free energy calculations->Proficiency in molecular modeling tasks such as homology modeling, conformation generation, core hopping, protein binding site analysis, and QM/MM (ONIOM) calculations->Well-versed in structure-based drug design techniques, including molecular docking methods like ensemble docking, induced fit docking, quantum polarized ligand docking, and structure-based virtual screening->Expertise in ligand-based drug design, covering areas such as pharmacophore modeling, 3D-QSAR, descriptor generation, ADME/Tox prediction, and ligand-based virtual screening methods->Thorough experience in utilizing Turbomole and Gaussian codes for quantum mechanics & Atom in Molecules (AIM) calculations, particularly for studying spectroscopic, catalysis, and self-assembly processes of inorganic-organic reactions and host-guest complexation->Worked on small molecule parameterization, including MM level parameterization of inorganic molecules and Coarse-grain (Martini) parameterization. Conducted validation and evaluation of thermochemical, geometrical, and volume-related properties->Practical experience working with high-performance computing (HPC) systems and advanced GPU-based workstations for conducting MD simulations and performing big data analysis.