Shamrat Kumar Paul

Bio

I am a PhD student in Medical Biophysics at Clemson University. I specialize in computational biophysics and the thermodynamics of biomolecules, with a dedicated focus on developing therapeutics for rare diseases—principally CDKL5 deficiency disorder.

I developed and maintain ColabMDA and am a core contributor to SAMPDI-3Dv2.

Research Interests

Rare-Disease Therapeutics: Investigating the molecular mechanisms of CDKL5 deficiency to identify novel treatment pathways.
Computational Biophysics & Thermodynamics: Modeling biomolecular interactions to understand stability and binding affinity.
Open-Source Tool Development: Creating accessible, high-performance workflows for the scientific community.

News

Feb 2026: Invited to present research on CDKL5 deficiency disorder at ACS Spring 2026 (March 22-26) in the COMP Division.
Aug 2025: Paper on CDKL5 Deficiency Disorder published in IJMS.
Dec 2024: SAMPDI-3Dv2 paper published in Genes.

Selected Publications

CDKL5 Deficiency Disorder: Revealing the Molecular Mechanism of Pathogenic Variants.

Paul, S.K., Panday, S.K., Boccuto, L., and Alexov, E.

International Journal of Molecular Sciences (2025)

PDF Journal
Further Development of SAMPDI-3D: Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA.

Rimal, P., Paul, S.K., Panday, S.K., and Alexov, E.

Genes (2025)

PDF Journal
Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice.

Paul, S.K., Saddam, M., Rahaman K.A., Choi, J.G., Lee, S. S., Hasan, M.

Heliyon (2022)

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