Indrajit Deb
University of Dundee, PharmCADD Co. Ltd., Michigan State University
0000-0002-2722-582X
About
➣ The domain of research is studying the conformational/structural, thermodynamic, kinetic, and equilibrium properties of nucleic acids, proteins, and nucleic acid-protein, RNA-ligand, and protein-ligand complexes; and computer-aided drug discovery starting from hit discovery to lead optimization in the process of structure-based and ligand-based drug development
➣ ML/DL approaches for DMPK property prediction, Uncertainty quantification
➣ Free energy calculation approaches
➣ Computational biomolecular modeling approaches, statistical mechanics, and conventional and enhanced-sampling molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations to characterize and study biomolecules and their complexes
➣ Molecular docking and modeling techniques to discover/design and optimize small molecule drugs and studying structure-activity/kinetics/thermodynamics relations (SAR/SKR/STR)
➣ Method development to aid the computational drug discovery campaign
➣ Applications of classical mechanical and high-throughput quantum mechanical (QM) calculations in drug development
➣ Physics-based classical force field parameter development approaches
➣ Extensive validation approaches for molecular mechanics force fields
➣ Modeling approaches to design and study the influence of post-transcriptionally and synthetically modified RNA residues on the structural and functional aspects of nucleic acid systems starting from mononucleoside to polynucleotide level, for instances di/trinucleotides, duplexes, hairpins, and quadruplexes and also in DNA-RNA hybrids like DNAZymes
➣ Molecular dynamics guided flexible fitting refinement and validation for the X-ray and cryo-EM maps and resolving of NMR structures using NMR restraints
Email: [email protected]
Google Scholar: https://scholar.google.com/citations?user=X8q6xHEAAAAJ&hl=en
Employment
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University of Dundee Senior Computational Chemist2023 - Present
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PharmCADD Co. Ltd. Senior Scientist2021 - 2023
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Michigan State University Postdoctoral Research Associate2020 - 2021
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University of Michigan Department of Biophysics Postdoctoral Research Fellow2017 - 2020
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Institute of Bioorganic Chemistry Polish Academy of Sciences Research Fellow2015 - 2016
Education
Education history is unavailable.
Projects & Funding
Projects & funding information is unavailable.
Publications (18)
- Structural and Thermodynamic Consequences of Base Pairs Containing Pseudouridine and N1‐methylpseudouridine in RNA Duplexes Save
- Structural and dynamic consequences of inosine, 2′-O-methylation, and N6-methyladenosine modifications in RNA G-quadruplex: A molecular dynamics study Save
- N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation Save
- Using Dynamic Interaction Fingerprints to Derive Baseline Machine Learning Model for the Prediction of Protein-Ligand Dissociation Rate Constant Save
- Quantum chemical and molecular modeling studies of twenty therapeutic nucleosides and nucleoside analogues Save
- Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes Save
- Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA Save
- Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives Save
- N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation Save
- Comparative Analysis of RNA Secondary Structure Accuracy on Predicted RNA 3D Models Save