Sunandan Mukherjee

Post-doctoral Scientist in Computational Structural Biology

International Institute of Molecular and Cell Biology (IIMCB), Warsaw, Poland

About Me

Dr. Sunandan Mukherjee

I am a post-doctoral scientist at the International Institute of Molecular and Cell Biology (IIMCB) in Warsaw, Poland, specializing in computational structural biology. My research focuses on developing and applying computational methods to understand the complex relationship between RNA sequence, structure, and function.

I completed my PhD at the Indian Institute of Technology Kharagpur in 2018, where I investigated the molecular mechanisms of RNA–protein interactions based on their physicochemical properties. This work laid the foundation for my current interests in applying machine learning to structural biology and developing computational tools for the scientific community.

My interdisciplinary approach blends computer science, biophysics, and molecular biology to address challenging problems in RNA research. I am passionate about building accessible tools that advance discoveries in structural biology.

Research Interests

  • RNA structure prediction & modeling (actively involved in RNA-Puzzles and CASP)
  • Integrative modeling of biomolecular structures with cryo-EM maps
  • Developing tools for macromolecular structures and interactions

Professional Experience

Postdoctoral Researcher

IIMCB, Warsaw, Poland

JULY 2018 – PRESENT

  • Developed and applied cutting-edge computational methods for RNA 3D structure prediction and refinement.
  • Collaborated with experimental groups to validate models against experimental data (cryo-EM, SAXS).
  • Contributed to understanding nucleic acid structural biology challenges.

Protein Engineering Specialist

Incircular BV, Amsterdam & IIMCB

MAY 2022 – OCT 2022

  • Led a project on Fast Monte Carlo dynamics simulations to assess protein thermal unfolding.
  • Analyzed the impact of crosslinker restraints on protein stability.

Institute Teaching Assistant

IIT Kharagpur, India

JAN 2016 – JAN 2018

  • Assisted in teaching Bioinformatics and Computational Biology courses to undergraduate and postgraduate students.

Junior Research Fellow

AIIMS, New Delhi, India

JUN 2011 – OCT 2011

  • Conducted clinical evaluation of a real-time PCR assay for detecting Chlamydia trachomatis.

Talks & Presentations

“Integrated modeling of RNA 3D structures with SimRNA-Cry”
EMBO Sectorial Meeting on RNA and Structural Biology, Würzburg, Germany, April 2025

"Modeling 3D structure of RNA using low resolution cryo-EM maps with SimRNA-Cry"
EMBO Workshop: Computational Structural Biology, EMBL Heidelberg, Germany, December 2023

“SimRNA-Cry: a tool for modeling of RNA molecules using maps from cryo-electron microscopy”
Symposium of Polish Bioinformatics Society 2022, Warsaw, Poland, September 2022

“Cluster and Rule: from the modeling perspective”
RNA-Puzzles meeting, IIMCB, Warsaw, Poland, December 2018

Research Impact

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Publications by Year

Skills & Expertise

Computational & Molecular Modeling

RNA/Protein 3D Modeling Molecular Dynamics (MD) Monte Carlo Simulations Integrative Modeling (cryo-EM, SAXS) Macromolecular Docking SimRNA-Cry

Programming & Data Science

Python C/C++ Bash R Scikit-learn TensorFlow

Tools & Platforms

Nextflow Snakemake Git (Gitlab, Github) Linux macOS Amber