Shamrat Kumar Paul

Shamrat Paul is a computational biophysicist and PhD candidate in Medical Biophysics at Clemson University. His research integrates molecular simulations, structural bioinformatics, and biomolecular thermodynamics to understand how disease-associated genetic variants alter protein structure, dynamics, and function. His work aims to connect these molecular mechanisms with rational therapeutic strategies, with a dedicated focus on CDKL5 Deficiency Disorder. He developed and maintains ColabMDA and is a contributor to SAMPDI-3Dv2. Read more

Shamrat Paul is a computational biophysicist and PhD candidate in Medical Biophysics at Clemson University. His research integrates molecular simulations, structural bioinformatics, and biomolecular thermodynamics to understand how disease-associated genetic variants alter protein structure, dynamics, and function. His work aims to connect these molecular mechanisms with rational therapeutic strategies, with a dedicated focus on CDKL5 Deficiency Disorder. He developed and maintains ColabMDA and is a contributor to SAMPDI-3Dv2.

His doctoral research in the Emil Alexov research group investigates how missense variants alter protein stability and partner binding, curates large variant datasets, and translates structure- and energy-based insights into rational strategies for variant-guided small-molecule discovery. He also works on machine-learning approaches to predict mutation effects on biomolecular interactions.

He recently presented a CDKL5 variant reclassification framework named cdkl5-variants that links variant impacts on folding and binding energetics to pathogenicity and highlights potential avenues for targeted therapy design, and develops automated workflows including VarMDyn to connect variants directly to molecular dynamics simulations.

He also holds an MS in Medical Biophysics from Clemson University and a BSc in Biochemistry and Molecular Biology from BSMRSTU, Bangladesh. His background spans molecular biology, physical chemistry, and computational modeling, which he combines to study biomolecular systems.

His 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. On October 20, 2026, he won first place at the Cooper Library Graduate Data Hackathon (CLGDH). Earlier, he received a GRIESHMA research fellowship at IIT Madras and was joint second runner‑up at the BAUET Tech Fair for research combining quantum chemistry with molecular docking. Show less