Postdoctoral Researcher @ Université Paris Cité & Université de La Réunion, France
🎓 PhD in Computational Structural Biology @ CSB Lab, Indian Institute of Technology Kharagpur
📖 PhD Thesis: "Conformational analysis of protein–RNA recognition" (Advisor: Prof. Ranjit P. Bahadur)
🎯 Research Focus: Protein–RNA recognition mechanisms, conformational selection & induced fit, RNA-binding protein rotamer libraries, RNA conformers, high-performance computing (HPC), and multi-microsecond molecular dynamics simulations.

My doctoral research centered on deciphering the molecular principles, conformational transitions, and energetics governing protein–RNA recognition across four major contributions:

• Overview: Developed a non-redundant, high-resolution protein–RNA docking benchmark dataset (version 3.0) integrated with experimental binding affinity ($\Delta G / K_d$).
• Significance: Provides the structural biology community with a standardized gold standard to evaluate rigid-body and flexible docking algorithms, scoring functions, and interface energetics.
• Publication: Proteins: Structure, Function, and Bioinformatics (2025) | DOI: 10.1002/prot.26825
• Repository: shrikantcombio/PRDBv3_dataset

• Overview: Built RNA-binding protein-specific Backbone-Dependent (BBD), Backbone-Independent (BBI), and Secondary Structure-Dependent (SSD) side-chain rotamer libraries.
• Significance: Characterized the side-chain conformational transitions that occur upon RNA binding, providing essential priors for accurate modeling of induced-fit side-chain adjustments in RBPs.
• Status: Nucleic Acids Research (2025, Submitted)
• Repository: shrikantcombio/RBPs_rotamer_lib

• Overview: Curated a structural library of RNA dinucleotide conformers in both bound and unbound protein–RNA complexes.
• Significance: Systematically decoded RNA backbone flexibility ($\alpha, \beta, \gamma, \delta, \epsilon, \zeta$) and glycosidic ($\chi$) torsion angles, uncovering the conformational selection vs. induced-fit dynamics of RNA in macromolecular recognition.
• Status: RNA Journal (2025, Under Revision) | BioRxiv: 10.64898/2026.05.14.725147
• Repository: shrikantcombio/RBPs_RNA_conformers_lib

• Overview: Applied multi-microsecond all-atom Molecular Dynamics simulations (using GROMACS & AMBER on IIT Kharagpur's Paramshakti supercomputer) to investigate non-canonical RBP recognition.
• Significance: Unraveled mutually induced conformational changes in the Ubiquitin-Like Domain (ULD) of SF3A1 recognizing the stem-loop 4 (SL4) of U1 snRNA during early spliceosome assembly.
• Status: Journal of Molecular Recognition (2026, Under Revision) | BioRxiv: 10.64898/2026.03.30.715355

Active computational platforms and toolkits currently under development:

1. Kant S, Chandran N, Mukherjee S, Maity A, Bahadur RP. (2025). Protein-RNA Docking Benchmark v3.0 integrated with Binding Affinity. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.26825
2. Mukherjee S*, Kant S*, Bahadur RP. (2025). Transition of side-chain conformations of RNA-binding proteins upon binding RNA. Nucleic Acids Research (Submitted). (*Joint first authors)
3. Kant S, Masipeddi S, Bahadur RP. (2025). Deciphering conformational preferences of RNA in protein-RNA recognition. RNA Journal (Under Revision). BioRxiv: 10.64898/2026.05.14.725147
4. Kant S. (2026). Decoding Mutually Induced Conformational Changes in Non-Canonical Recognition of U1 SL4 snRNA by ULD of SF3A1 during Early Spliceosome Assembly. Journal of Molecular Recognition (Under Revision). BioRxiv: 10.64898/2026.03.30.715355
5. Garai S, Kant S, Bahadur RP. (2026). An atlas of non-redundant sequences and structures of transcription factor assemblies across domains of life. Journal of Structural Biology, 108369. DOI: 10.1016/j.jsb.2026.108369 | [Webserver]
6. Verma J, Jain D, Panda AP, Kant S, Kumar G, Ghosh AS. (2023). Involvement of non-active site residues in the catalytic activity of NDM-4 Metallo beta-lactamase. The Protein Journal. DOI: 10.1007/s10930-023-10124-6
7. Agarwal A, Kant S, Bahadur RP. (2023). Efficient mapping of RNA-binding residues using local sequence features in protein-RNA complexes. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.26528
8. Agarwal A, Alagar S, Kant S, Bahadur RP. (2023). Binding dynamics of tandem RNA recognition motifs (tRRMs) of HuR with mRNA. Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2022.2073270
9. Agarwal A, Singh K, Kant S, Bahadur RP. (2022). Comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. Computational and Structural Biotechnology Journal. DOI: 10.1016/j.csbj.2022.06.036

• Programming & Scripting: Python, C, C++, R, Bash / Shell Scripting
• Molecular Dynamics Simulations: GROMACS, AMBER, VMD, trajectory analysis pipelines
• Structural Bioinformatics & Modeling: NACCESS, HBPLUS, x3dna-dssr, DSSP, US-align, TM-align, MMseqs2, MODELLER, PyMOL, ChimeraX
• High-Performance Computing (HPC): Slurm workload manager, parallel job arrays, Paramshakti Supercomputer (National Supercomputing Mission, NSM)
• Machine Learning & Data Science: Scikit-learn, PyTorch, NumPy, Pandas, SciPy, Matplotlib, Seaborn
• Web Development & Databases: Django, HTML/CSS, PHP, MySQL, Apache, REST APIs
• Environments: Linux (Ubuntu, CentOS), Git, GitHub Actions, Docker

• Postdoctoral Researcher – Université Paris Cité & Université de La Réunion, France
• Travel Grant – 13th RNA India Meeting (2026), IISc Bengaluru
• Travel Grant – EMBL Conference: The Expanding World of RBPs (2025), Heidelberg, Germany
• Fully Funded Fellow – EMBO Workshop on Computational Structural Biology (2023), Heidelberg, Germany
• Institute Research Fellowship – Indian Institute of Technology (IIT) Kharagpur (2018–2024)
• All India Rank (AIR) 4 – DBT Computational Biology Entrance Examination

• 🌐 Personal Website: https://shrikantcombio.github.io/
• 🏛️ Current Affiliation 1: Université Paris Cité & Université de La Réunion, France
• 🏛️ Current Affiliation 2: National Centre for Biological Sciences (NCBS), TIFR, Bangalore
• 🎓 Alma Mater: CSB Lab, Indian Institute of Technology Kharagpur
• 📬 Email: shrikant92pharmacy@gmail.com
• 💼 LinkedIn: Shri Kant, PhD
• 🐙 GitHub Profile: @shrikantcombio

"Decoding the structural dynamics and energetics of biomolecular recognition through computation and algorithms."