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Happy coding...!!!
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Happy coding...!!!
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shrikantcombio/README.md

Hi there, I'm Dr. Shri Kant 👋 🔬

Postdoc NCBS TIFR PhD IIT Kharagpur GitHub PRince Email

Postdoctoral Researcher @ National Centre for Biological Sciences (NCBS), TIFR, Bangalore
🎓 PhD in Computational Structural Biology @ CSB Lab, IIT Kharagpur
Focused on Structural Bioinformatics, Biomolecular Interactions (Protein-RNA/DNA/Ligand), Macromolecular SASA & Energetics, and Machine Learning in Computational Biology.

🔬 Research Focus & Areas of Interest

  • 🧬 Biomolecular Interface Analysis: SASA, Buried Surface Area (BSA), Local Packing Density (LD), Hydrogen Bonding, and Water Bridge Networks in Protein-RNA/DNA/Ligand complexes.
  • 💻 High-Performance Scientific Computing: C/C++ & Python package development for large-scale structural dataset extraction (PDB & mmCIF format processing).
  • 🤖 Machine Learning in Structural Biology: Predictive modeling of Transcription Factor non-redundant datasets (TF-NRD) and macromolecular interaction dynamics.
  • 📐 Rotamer & Structural Analysis: Advanced rotamer assignment and conformational analysis in proteins and nucleic acids.

🚀 Featured Open-Source Projects

Repository Description Technologies
👑 PRince Modernized C-based automated interface & interaction calculator for Protein-Protein, Protein-RNA, Protein-DNA, and Protein-Ligand complexes (PDB & mmCIF support). C99, Python, NACCESS, HBPLUS, Bash
📊 TF-NRD Analysis Transcription Factor Non-Redundant Dataset interface property extraction and multi-sheet analysis suite. Python, Pandas, OpenPyXL, Biopython
🔄 Rota-Assign Utilities Rotamer assignment, mmCIF duplicate cleaning, and structural reader utilities. Python, Bio.PDB, mmCIF

🛠️ Tech Stack & Technical Expertise

  • Languages: C, C++, Python, Bash / Shell Scripting, R
  • Bioinformatics & Structural Tools: NACCESS, HBPLUS, PyMOL, DSSP, HSSP, Bio.PDB, OpenMM
  • Data Science & ML: NumPy, Pandas, Scikit-learn, PyTorch, Matplotlib, Seaborn
  • Development & Build Systems: Git, GitHub Actions, Linux Systems Administration, Makefile, CMake

📈 GitHub Statistics & Language Distribution

Dr. Shri Kant's GitHub Stats Top Languages

📫 Connect & Collaboration

"Decoding biomolecular recognition through structure, algorithms, and data."

Pinned Loading

  1. PRDBv3_dataset PRDBv3_dataset Public

    Protein-RNA docking benchmark v3.0

    Jupyter Notebook 2

  2. gmx_MMPBSA_dataParser gmx_MMPBSA_dataParser Public

    For the independent analysis of the different binding free energy files generated by the gmx_MMPBSA such as a CSV and DAT files.

    Jupyter Notebook

  3. RBPs_RNA_conformers_lib RBPs_RNA_conformers_lib Public

    RNA backbone has six degrees of freedom and side-chain adopts different orientation these make RNA molecule more flexible compared to proteins.

  4. RBPs_rotamer_lib RBPs_rotamer_lib Public

    Backbone dependent RNA binding proteins specfific rotamer library created for the resideus present at the interface, non-interface and overall surface residues.

    Python

  5. RNAmodViz RNAmodViz Public

    RNAmodViz is a lightweight toolkit for the retrieval, parsing, visualization, and cataloging of modified RNA nucleotides from the Protein Data Bank (PDB) Chemical Component Dictionary (CCD).

    Jupyter Notebook