Thirumal Kumar D

Structural Biologist / Computational Biologist / Bioinformatician

He is currently engaged in the Computer Aided Drug Designing (CADD) aspects. He has hands-on experience with many of the computational packages. Few of them are as follows:

GROMACS (GRoningen MAchine for Chemical Simulations) – is a molecular dynamics package mainly designed for simulations of the proteins, lipids, and nucleic acids.

Desmond Schrodinger – is a high-speed molecular dynamics simulation package.

AMBER (Assisted Model Building with Energy Refinement) – is a biomolecules simulation package.

AutoDock– is a molecular docking software, especially for protein-ligand.

I-TASSER (Iterative Threading ASSEmbly Refinement) – is an approach to model protein structure and function prediction.

MODELLER – is a standalone package for homology modeling.

HADDOCK – a software to study the protein-protein interaction and bindings.

MEGA – a computational package to analysis the phylogeny relationship across the species.

 

RESEARCH INTEREST:

  • Computational analysis of disease-related Single Nucleotide Polymorphisms (SNPs)

  • Molecular dynamics simulation studies.

  • Molecular modeling and docking analysis.

  • Medical Informatics

  • Single amino acid substitutions (SAPs)

  • In-silico drug designing.

  • Biological database development.

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TECHNICAL SKILLS:

  • Operating Systems – Windows & Linux (Ubuntu, openSUSE)

  • Molecular Dynamics Simulation – GROMACS, AMBER, Schrodinger Desmond

  • Molecular Docking – AutoDock, AutoDock Vina, GOLD Suite, Online HADDOCK

  • Molecular Modeling – Modeller, I-Tasser, Swiss Model

  • Phylogenetic Analysis – MEGA.

  • Web biological tools – BLAST, Clustal Omega, SIFT, polyphen, I mutant, SNAP, SNPs&go, FATHMM, Align GVGD, SNP effect, cupsat, iStable, MUpro, PANTHER

  • Biological Databases – SwissProt, UniProt, NCBI, HGMD, PDB

  • Visualization tools – PyMOL, Chimera, Schrodinger Maestro, Discovery Studio Visualizer

  • Editors – Microsoft Office, LATEX, Adobe PhotoShop, Smart Draw, Visio

  • Website designing software – WebPlus, ASP Maker, PHP Maker, WordPress