Welcome to the Chakrabarty Lab

Computational Molecular Biophysics & Theoretical Physical Chemistry Group
S. N. Bose National Centre for Basic Sciences, Kolkata, India

From Molecules to Mechanisms: Connecting Thermodynamics, Dynamics, and Function

Grounded in statistical mechanics and molecular thermodynamics, our research operates at the intersection of chemistry, physics, biology, and data science. We develop and apply advanced computational strategies—from classical molecular dynamics to machine-learning-assisted enhanced sampling methods—to understand the structure, dynamics, and function of complex (bio)molecular systems.

Our research covers a broad spectrum of problems, ranging from the fundamental physical chemistry of small molecules to the intricate conformational landscapes of biomacromolecules and self-assembled materials.

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Recent Highlights

  • Awards: Prof. Suman Chakrabarty has been honored with the Dr. APJ Abdul Kalam HPC Award 2025 (Researcher - R&D in HPC Applications) and the Chemical Research Society of India (CRSI) Bronze Medal Award 2025.
  • New Methods: Our group has recently released CoWERA (2026) and PathGennie (2025), advanced tools designed for binless resampling in weighted-ensemble simulations and rare-event pathway generation.
Research

Our research focuses on the intersection of computational molecular biophysics and theoretical physical chemistry. We design and apply advanced computational approaches grounded in statistical mechanics and molecular thermodynamics to tackle challenging, interdisciplinary problems across chemistry, physics, and biology. The overarching aim is to gain a molecular-level understanding of how interactions and dynamics drive emergent functions and material properties. We employ molecular simulations, enhanced-sampling strategies, and machine-learning-based methods to investigate complex biomolecular and soft-matter systems — spanning small molecules, interfacial water, large proteins and enzymes, to self-assembled proteins. Our current research themes include (bio)molecular recognition and allostery, machine-learned discovery of collective variables for rare-event sampling, mechanistic studies of phase transitions, protein folding and aggregation, and AI-driven exploration of free-energy landscapes.

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Allostery, Signalling & Protein–Protein Interactions

Allostery, Signalling & Protein–Protein Interactions

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Enhanced Sampling & Machine Learning

Enhanced Sampling & Machine Learning

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Folding, Misfolding & Enzyme Catalysis

Folding, Misfolding & Enzyme Catalysis

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Water, Hydration & Solvation

Water, Hydration & Solvation

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Soft Matter, Self-Assembly & Interfaces

Soft Matter, Self-Assembly & Interfaces

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Selected Publications

Hidden electrostatic basis of dynamic allostery in a PDZ domain
Hidden electrostatic basis of dynamic allostery in a PDZ domain

A Kumawat, S Chakrabarty, Proc. Natl. Acad. Sci. USA 114, E5825 (2017).

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PathGennie: Rapid Generation of Rare Event Pathways via Direction-Guided Adaptive Sampling Using Ultrashort Monitored Trajectories
PathGennie: Rapid Generation of Rare Event Pathways via Direction-Guided Adaptive Sampling Using Ultrashort Monitored Trajectories

Dibyendu Maity, Shaheerah Shahid, Suman Chakrabarty, J. Chem. Theory Comput. 21, 11377–11389 (2025).

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IceCoder: Identification of Ice phases in molecular simulation using variational autoencoder
IceCoder: Identification of Ice phases in molecular simulation using variational autoencoder

D Maity, S Chakrabarty, J. Chem. Theory Comput. 21, 1916 (2025).

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Phosphorylation induces altered protonation states and allosterically regulates Rac1–RhoGDI complex
Phosphorylation induces altered protonation states and allosterically regulates Rac1–RhoGDI complex

Krishnendu Sinha, Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty, Protein Science 35, e70413 (2026).

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CoWERA: A temporal coherence guided binless resampling algorithm for weighted-ensemble based estimation of rare-event kinetics
CoWERA: A temporal coherence guided binless resampling algorithm for weighted-ensemble based estimation of rare-event kinetics

Shaheerah Shahid, Dibyendu Maity, Suman Chakrabarty, J. Chem. Phys. 164, 134111 (2026).

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PPIscout: Protein–protein interaction site hotspot mapping using mixed amino acid–water molecular dynamics simulation
PPIscout: Protein–protein interaction site hotspot mapping using mixed amino acid–water molecular dynamics simulation

Sutanu Mukhopadhyay, Suman Chakrabarty, J. Chem. Sci. 137, 106 (2025).

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Recent Publications

Mapping Protein–Protein Interaction Hotspots and Unveiling a Cryptic Allosteric Pocket in PLK1 PBD via Mixed-Solvent Molecular Dynamics
Mapping Protein–Protein Interaction Hotspots and Unveiling a Cryptic Allosteric Pocket in PLK1 PBD via Mixed-Solvent Molecular Dynamics

Sutanu Mukhopadhyay, Suman Chakrabarty, Chem. Phys. Chem. 27, e202500907 (2026).

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CoWERA: A temporal coherence guided binless resampling algorithm for weighted-ensemble based estimation of rare-event kinetics
CoWERA: A temporal coherence guided binless resampling algorithm for weighted-ensemble based estimation of rare-event kinetics

Shaheerah Shahid, Dibyendu Maity, Suman Chakrabarty, J. Chem. Phys. 164, 134111 (2026).

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Transgenic Tobacco Plants Expressing Synthetic Peptides: A Functional and Structural Analysis for Pathogen Resistance
Transgenic Tobacco Plants Expressing Synthetic Peptides: A Functional and Structural Analysis for Pathogen Resistance

Karishma Biswas, Sudipta Mitra, Dibakar Roy, Sanhita Roy, Dibakar Sarkar, DeokHyun Son, Rohit Das, Anuradha Roy, Dulal Senapati, Humaira Ilyas, A. Harikishore, Ranjit Biswas, Suman Chakrabarty, ..., Plant Biotechnology Journal 24, 526 (2026).

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Phosphorylation induces altered protonation states and allosterically regulates Rac1–RhoGDI complex
Phosphorylation induces altered protonation states and allosterically regulates Rac1–RhoGDI complex

Krishnendu Sinha, Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty, Protein Science 35, e70413 (2026).

View Paper
PPIscout: Protein–protein interaction site hotspot mapping using mixed amino acid–water molecular dynamics simulation
PPIscout: Protein–protein interaction site hotspot mapping using mixed amino acid–water molecular dynamics simulation

Sutanu Mukhopadhyay, Suman Chakrabarty, J. Chem. Sci. 137, 106 (2025).

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Media Highlights

New computational method “Fast-Tracks” drug discovery
New computational method “Fast-Tracks” drug discovery
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Substrate promiscuity of fungi generated enzyme Laccase shows potential in degrading industrial dye effluents
Substrate promiscuity of fungi generated enzyme Laccase shows potential in degrading industrial dye effluents
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New artificial light-harvesting system using organic nanotubes useful for solar cells, photocatalysis, optical sensors & tunable multi-color light emitting materials
New artificial light-harvesting system using organic nanotubes useful for solar cells, photocatalysis, optical sensors & tunable multi-color light emitting materials
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Explore Opportunities

Whether you are looking for a PhD position, Postdoctoral Fellowship, or a short-term Project Internship, discover all our current openings and admission details in one place.

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