Our Dry-Lab basically constitutes three important aspects - Molecular Docking, Molecular Dynamics Simulations and Simulation Analysis of Protein-DNA Aptamer. For Molecular Docking, we firstly conducted Pre-Docking Processing to obtain 2-D, 3-D structure of DNA Aptamer from its sequence, and then conduct docking exercise for the same with Protein using HADDOCK Web server, and its Protein-Nucleic Acid software to conduct the exercise.

With that, we generate the Input files for the Molecular Dynamics Simulation using GROMACS, with the help of CHARMM-GUI, a HARVARD Web Server, for the above process that includes files for EM run, NVT and NPT run culminating in the MD run. We use GROMACS installed in the Linux-Ubuntu system and adjust the simulation time to 50ns and 100 ns respectively for the larger and shorter proteins respectively. Post-Simulation we analyze the data for RMSD, RMSF, Radius of Gyration, Energy, and H-Bonds along with Secondary Structure count. With the help of these, we can conduct studies for Aptamer-Protein analysis to complement Wet-Lab experiments and conclude the best-Aptamers, confirmations and possible Mutation sites for modified, advanced Aptamers for our POC kit.