I am a PhD student in Medical Biophysics in the Department of Physics & Astronomy at Clemson University, here in beautiful Clemson, South Carolina, USA. I also hold an MS in Medical Biophysics from Clemson University and a BSc in Biochemistryfrom BSMRSTU, Bangladesh. My background spans molecular biology, physical chemistry, and computational modeling, which I combine to study biomolecular systems.
My doctoral research focuses on biophysics, thermodynamics of biomolecules and computation with an emphasis on rare-disease therapeutics development, especially targeting CDKL5 deficiency disorder. I investigate how missense variants alter protein stability and partner binding, curate large variant datasets, and translate structure- and energy-based insights into ideas for variant-guided small-molecule discovery. I also work on machine-learning approaches to predict mutation effects on biomolecular interactions.
I develop and share open-source tools that make computational workflows more accessible. Notable projects include ColabMDA, which streamlines molecular dynamics on Google Colab, and contributions to SAMPDI-3Dv2 for mutation-effect prediction in Protein-DNA complex. I recently presented a CDKL5 variant reclassification framework named cdkl5-variants that links variant impacts of folding and binding energetics to pathogenicity and highlights potential avenues for targeted therapy design.
My work has been supported by several fellowships, including the Clemson Graduate Education Program Quasi‑Endowment (College of Science fellowship) and the Pearce Center Grad WAC Fellowship. Earlier I received a GRIESHMA research fellowship at IIT Madras and was joint second runner‑up at the BAUET Tech Fair for a project combining quantum chemistry with docking.
My open-source work lives on GitHub. I welcome collaboration and questions. Connect with me on LinkedIn. To browse selected work, visit the Projects page. Reach me at shamrap@clemson.edu.