Blog 2 – Using Charmm-GUI: Combining Docking, Molecular Dynamics Simulation, and Free Energy Calculation to Improve the Accuracy of Virtual Screening of Anticancer Drug Candidates Against Human Telomeric G-quadruplex DNA

Previous issues that Dr. Deng’s research has encountered include inaccurate 3D visualization of results. This issue is not due to incorrect input or human error, but rather due to the limited abilities/extent of the algorithm in molecular docking programs previously used. To solve this issue, we are currently trying to utilize a different molecular docking program called Charmm-GUI. Charmm-GUI is designed to “interactively build complex systems and prepare their inputs with well-established and reproducible simulation protocols for state-of-the-art biomolecular simulations” (as described by its official website). In coordination with widely used simulation packages such as CHARMM, AMBER, NAMD, GROMACS, GENESIS, LAMMPS, Desmond, and OpenMM, Charmm-GUI is a very promising platform whose more streamlined interface will hopefully provide more accurate results for our virtual screening of anticancer drug candidates against human telomeric G-quadruplex DNA.

Work for this project under Dr. Deng has been going smoothly so far. Regular communication has been crucial, and I am fortunate that Dr. Deng is always available to provide insight and tips in the learning process for this new molecular docking program and the overall problem-solving process. We plan on continuing research during Winter Break going into the Spring Semester, during which we hope to obtain final results.

Leave a Reply

Your email address will not be published.