Dr. Faisal Ahmad

I am a Computational Microbiology researcher with a background in general microbiology and molecular bacteriology/viruses and cancer genomics. My research interests include molecular docking and molecular dynamics simulations of proteins/DNA/RNA and Lipid bilayer to better understand their structural and dynamical features in the biological system. I have also interested in predicting protein-ligand binding free energy using various methods such as QM/MM Molecular Dynamics Simulations, MMGB/PBSA, Liner Interaction Energies, Thermodynamics Integration, Free Energy Perturbation, Bennet’s, and Water Swap methods. I have extensive experience in utilizing various computational tools and software packages, such as molecular docking (GOLD, Discovery Studio), molecular dynamics simulations (AMBER, CHARM, GROMACS, DESMOND, SILCS), binding free energy calculation, axial frequency distribution and quantum chemical calculations, to design and optimize drug candidates. Another line of my research is exploring bacterial genomes through subtractive proteomics and immune-informatics approaches to identify essential drug and vaccine targets and to filter non-essential drug targets for anti-virulent compounds development. I am interested in using system biology approaches for the design of subunit and peptide-based vaccine candidates against infectious pathogens. My recent interests are in viral and bacterial database development to assist researchers in the field of therapeutics development. I have a good knowledge of animal model studies and work in close collaboration with experimentalists on topics like antibiotics resistance, mutational studies, metagenomics, and expression data. I conducted broad research on mathematical modeling of sputum and saliva microbiome analysis, with a particular focus on using computational approaches to understand the complex interactions between microbial communities and their host environment.