Publications

Our Publications

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).

View Paper
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).

View Paper
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).

View Paper
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
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).

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).

View Paper

All publications

For citation metrics, please visit our Google Scholar page.

Structural heterogeneity defines the allosteric landscape and conformational selection mechanism of the PDZ2 domain

Sreyan Bhowmick, Krishnendu Sinha, Suman Chakrabarty

Physical Chemistry Chemical Physics (2026).

View →
Microwave-assisted thermal profiling of blood: a potential biomarker for differentiating cancer and non-cancer states

Subhasish Sarkar, Ritabrata Saha, Avishek Dutta, Rik Chattopadhyay, Dibyendu Maity, Indranil Biswas, Arup Mondal, Abhik Ghosh, Ranjan Ganguly, Apurba K Santra, Utpal Garain, Debasis Mitra, Suman Chakr

Journal of Medical Engineering & Technology (2026).

View →
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).

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).

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).

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).

Harnessing Allostery to Modulate Protein-Protein Interactions: From Function to Therapeutic Innovations

Sutanu Mukhopadhyay, Krishnendu Sinha, Suman Chakrabarty

J. Mol. Biol. 437, 169382 (2025).

View →
Unraveling antibody‐induced mechanical stability of antigen: Insights from single‐molecule studies

Soham Chakraborty, Shivam Pandit, Krishnendu Sinha, Madhu Bhatt, Debojyoti Chowdhury, Suman Chakrabarty, Shubhasis Haldar

Protein Science 34, e70201 (2025).

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

D Maity, S Chakrabarty

J. Chem. Theory Comput. 21, 1916 (2025).

Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De) stabilization Behavior

R Saha, S Chakraborty, K Sinha, P Pyne, S Pal, A Barman, S Chakrabarty, ...

J. Phys. Chem. Lett. 15, 10341 (2024).

View →
Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids

D Ray, D Chamlagai, S Kumar, S Mukhopadhyay, S Chakrabarty, ...

J. Phys. Chem. B 128, 6622 (2024).

View →
Conformational Effects on the Absorption Spectra of Phytochromes

S Santra, RN Manna, S Chakrabarty, D Ghosh

J. Phys. Chem. B 128, 3614 (2024).

View →
Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

K Sinha, A Kumawat, H Jang, R Nussinov, S Chakrabarty

Biophys. J. 123, 57 (2024).

View →
Phosphorylation-Competent Metastable State of Escherichia coli Toxin HipA

B Pandey, K Sinha, A Dev, HK Ganguly, S Polley, S Chakrabarty, G Basu

Biochemistry 62, 989 (2023).

View →
Efficient light harvesting in self-assembled organic luminescent nanotubes

SK Bhaumik, D Maity, I Basu, S Chakrabarty, S Banerjee

Chem. Sci. 14, 4363 (2023).

View →
Traceless cysteine-linchpin enables precision engineering of lysine in native proteins

NC Reddy, R Molla, PN Joshi, S TK, I Basu, J Kawadkar, N Kalra, ...

Nature Communications 13, 6038 (2022).

View →
Therapeutic opportunities of surface-active ionic liquids: a case study on acetylcholinesterase, citrate synthase and HeLa cell lines

P Baruah, D Ray, I Konthoujam, A Das, S Chakrabarty, K Aguan, S Mitra

New Journal of Chemistry 46, 20419 (2022).

View →
Heterogeneous nucleation in citrate synthesis of AgNPs: Effect of mixing and solvation dynamics

JB Deshpande, S Chakrabarty, AA Kulkarni

Chemical Engineering Journal 421, 127753 (2021).

View →
Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

M Santra, A Seal, K Bhattacharjee, S Chakrabarty

J. Chem. Phys. 154, 215101 (2021).

View →
Organoselenium compounds as acetylcholinesterase inhibitors: Evidence and mechanism of mixed inhibition

A Kumawat, S Raheem, F Ali, TA Dar, S Chakrabarty, MA Rizvi

J. Phys. Chem. B 125, 1531 (2021).

View →
Effect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study

N Choudhary, VR Hande, S Roy, S Chakrabarty, R Kumar

J. Phys. Chem. B 122, 6536 (2018).

View →
Soluble polybenzimidazoles with intrinsic porosity: Synthesis, structure, properties and processability

V Kumar, S Chatterjee, P Sharma, S Chakrabarty, CV Avadhani, ...

J. Polym. Sci., Part A: Polym. Chem. 56, 1046 (2018).

View →
Molecular View of CO2 Capture by Polyethylenimine: Role of Structural and Dynamical Heterogeneity

P Sharma, S Chakrabarty, S Roy, R Kumar

Langmuir 34 (17), 5138-5148, 2018 (2018).

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

A Kumawat, S Chakrabarty

Proc. Natl. Acad. Sci. USA 114, E5825 (2017).

Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach

S Bose, S Chakrabarty, D Ghosh

J. Phys. Chem. B 121, 4790 (2017).

View →
Molecular dynamics simulation and experimental study on the growth of methane hydrate in presence of methanol and sodium chloride

N Choudhary, OS Kushwaha, G Bhattacharjee, S Chakrabarty, R Kumar

Energy Procedia 105, 5026-5033, 2017 (2017).

View →
Mechanism of unfolding of human prion protein

RK Singh, NG Chamachi, S Chakrabarty, A Mukherjee

J. Phys. Chem. B 121, 550 (2017).

View →
Modeling gating charge and voltage changes in response to charge separation in membrane proteins

I Kim, S Chakrabarty, P Brzezinski, A Warshel

Proc. Natl. Acad. Sci. USA 111, 11353 (2014).

View →
Interplay between crystallization and glass transition in binary Lennard-Jones mixtures

A Banerjee, S Chakrabarty, SM Bhattacharyya

J. Chem. Phys. 139, 104501 (2013).

View →
Capturing the energetics of water insertion in biological systems: The water flooding approach

S Chakrabarty, A Warshel

Proteins: Struct. Funct. Bioinf. 81, 93 (2013).

View →
Realistic simulation of the activation of voltage-gated ion channels

A Dryga, S Chakrabarty, S Vicatos, A Warshel

Proc. Natl. Acad. Sci. USA 109, 3335 (2012).

View →
Coarse grained model for exploring voltage dependent ion channels

A Dryga, S Chakrabarty, S Vicatos, A Warshel

Biochim. Biophys. Acta - Biomembranes 1818, 303 (2012).

View →
Understanding Nucleation Phenomena at Large Metastability: From Gas Liquid to Metastable Solids and Polymers

M Santra, RS Singh, S Chakrabarty, B Bagchi

Nanoparticle Assembly: From Fundamentals to Applications, 15, 2011 (2011).

View →
Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects

AL Johansson, S Chakrabarty, CL Berthold, M Högbom, A Warshel, ...

Biochim. Biophys. Acta - Bioenergetics 1807, 1083 (2011).

View →
Anomalous behavior of linear hydrocarbon chains in water–DMSO binary mixture at low DMSO concentration

R Ghosh, S Banerjee, S Chakrabarty, B Bagchi

J. Phys. Chem. B 115, 7612 (2011).

View →
Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

S Chakrabarty, I Namslauer, P Brzezinski, A Warshel

Biochim. Biophys. Acta - Bioenergetics 1807, 413 (2011).

View →
Gas-liquid nucleation in a two dimensional system

M Santra, S Chakrabarty, B Bagchi

J. Chem. Phys. 129, 234704 (2008).

View →
Chakrabarty, Santra, and Bagchi Reply

S Chakrabarty, M Santra, B Bagchi

Physical Review Letters 101 (1), 019602, 2008 (2008).

View →
Elucidating the mechanism of nucleation near the gas-liquid spinodal

P Bhimalapuram, S Chakrabarty, B Bagchi

Phys. Rev. Lett. 98, 206104 (2007).

View →
Universal power law in the orientational relaxation in thermotropic liquid crystals

D Chakrabarti, PP Jose, S Chakrabarty, B Bagchi

Phys. Rev. Lett. 95, 197801 (2005).

View →