The research interest of Prof. Srabani Taraphder centers around computer simulation studies of simple charge transfer reactions in complex environment such as enzymes, their mutational variants and functionalized carbon nanotubes. The group has developed and used extensive computational methods of studying proton transfer reactions using a wide range of simulation methods including: classical and quantum mechanical-molecular mechanical (QM-MM) molecular dynamics simulations; Monte Carlo sampling of high dimensional protein conformational space; Transition path sampling simulations of rare dynamical events in proteins; Determination of reaction coordinates using machine learning based methods; Estimation of free energy and rate along the reaction coordinate of conformational transitions; Multi-dimensional property space analysis for classification of folded and unfolded conformations of proteins; Path search analysis in multi-dimensional property space. Our major aim is to elucidate the structure-function relationship of proteins and nanoscale systems in terms of the overall free energy cost of a reaction catalyzed/supported by these systems.
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In silico approaches to biomacromolecules through conformational dynamics and catalysis by Rai D., Khatua S., Paul T.K., Taraphder S. In-Silico Approaches to Macromolecular Chemistry - (Accepted/In-Press)
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pH-Dependent Structure and Dynamics of the Catalytic Domains of Human Carbonic Anhydrase II and IX by Taraphder S., Rai D. , Mondal D. Journal of Physical Chemistry B 127 10279-10294 (2023)
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Dynamics of the Conformation Dependent Unbinding of an Inhibitor of Ribonuclease A by Taraphder S., Dasgupta S. , Priyadarsinee S. Chemical Physics Impact - (Accepted/In-Press)
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Exploring the conformation-dependent reactivity and dynamics of a dinucleotide inhibitor of ribonuclease A by Priyadarsinee S., Das A., Taraphder S. Physical Chemistry Chemical Physics - (2026)
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Effect of Glycosylation on the Reorganization at the Active Site of Human Carbonic Anhydrase IX by Dey R., Shukla K., Das A., Taraphder S. ChemPhysChem 26 e2025005- (2025)
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Enhanced Sampling and Conformation-Dependent pKa of Histidine Side Chains: A Case Study in Human Carbonic Anhydrase II by Mondal D., Taraphder S. Journal of Chemical Theory and Computation 21 7131-7148 (2025)
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Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX by Dey R., Taraphder S. Journal of Physical Chemistry B 128 11054-11068 (2024)
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Structure and non-reactive dynamics of the dimeric catalytic domain of human carbonic anhydrase IX by Rai D., Taraphder S. Chemical Physics Impact 8 100625- (2024)
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A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II by Khatua S., De Bhowmik T., Taraphder S. ChemPhysChem e2022007- (2023)
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Dynamics of an inhibitor at and away from an out-of-active site binding location in human carbonic anhydrase II by Taraphder S., Khatua S. Chemical Physics Impact 7 100329-100329 (2023)
Principal Investigator
- Reactive Networks and Dynamics of Catalysis by the Cancer Related Enzyme Human Carbonic Anhydrase IX Anusandhan National Research Foundation (ANRF)
Ph. D. Students
Bhrigu Chakraborty
Area of Research: Computational Chemistry
Dulal Mondal
Area of Research: Computer Simulation Studies of Complex Systems
Kriti Shukla
Area of Research: Computer Simulation Studies of Complex Systems
Ritwika Dey
Area of Research: Bioorganic Chemistry
Sudipti Priyadarsinee
Area of Research: Biophysical Chemistry
