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 Rai D., Khatua S., Paul T.K., Taraphder S. By In-Silico Approaches to Macromolecular Chemistry 265-312 (2023)
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Unfolding intermediates of the mutant His-107-Tyr of human carbonic anhydrase II Taraphder S., Halder P. , Paul T. K., Khatua S. By Journal of Chemical Sciences (Special Issue on Theoretical Chemistry/Chemical Dynamics) (Invited article) 129 1031-1044 (2017)
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A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II Khatua S., De Bhowmik T., Taraphder S. By ChemPhysChem - (2023)
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Structure and Dynamics of the Isozymes II and IX of Human Carbonic Anhydrase Rai D., Khatua S., Taraphder S. By ACS Omega 7 31149-31166 (2022)
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In the Footsteps of an Inhibitor Unbinding from the Active Site of Human Carbonic Anhydrase II Taraphder S., Khatua S. By Journal of Biomolecular Structure and. Dynamics 41 3187-3204 (2023)
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Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction Paul T.K., Taraphder S. By Journal of Physical Chemistry B 126 1413-1425 (2022)
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Molecular modelling of two coordination states of Zn(II) ion at the active site of human carbonic anhydrase II Paul T.K., Taraphder S. By Chemical Physics 549 - (2021)
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Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II Paul T. K., Taraphder S. By ChemPhysChem 21 1455-1473 (2020)
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Novel Thiazoline-phenothiazine Based Push-Pull Molecules as Fluorescent Probes for Volatile Acids Detection Chaudhury S., Mukherjee M. , Paul T. K., Taraphder S. , Milton M. By J. Photochem. PhotoBiol. A: Chemistry 397 112509- (2020)
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Reaction Coordinate, Free Energy and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II Taraphder S., Paul S. , Paul T. K. By Journal of Physical Chemistry B 122 2851-2866 (2018)
Principal Investigator
- Computer Simulation Studies on the pH Dependent Structure and Dynamics of Carbonic Anhydrase IX
Ph. D. Students
Divya Rai
Area of Research: Theoretical Physical Chemistry
Dulal Mondal
Area of Research: Computer Simulation Studies of Complex Systems
Kangkan Pradhan
Area of Research: Theoretical Physical Chemistry
Kriti Shukla
Area of Research: Computer Simulation Studies of Complex Systems
Piyasi Garai
Area of Research: Computer Simulation Studies of Proteins
Ritwika Dey
Area of Research: Bioorganic Chemistry
