Author

Tarak Karmakar

Indian Institute of Technology DelhiORCID 0000-0002-8721-6247Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biophysics· 2

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 2 Research Focus:benchmarking· 1 Approach:biophysical modeling· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Assay:protein sequence· 1 Assay:protein structure· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Nisha KumariiD· 2 shared Shilpi SinghiD· 1 shared Sonam SonamiD· 1 shared Tanmay DuttaiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

4 top collaborators · 4 mutual co-author links

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2 shared papersBiophysics

Nisha KumariORCID

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2 papers

Recent·Most cited

BiophysicsJournal of Chemical Information and ModelingPeer-reviewedSep 17, 2025

Understanding RNA Chaperone Activity of ProQ Protein

Shilpi Singh, Nisha Kumari, Tanmay Dutta, Tarak Karmakar

This study investigates the RNA-binding mechanism of ProQ using molecular dynamics simulations, revealing electrostatic interactions and structural changes upon raiZ RNA binding.

3 citations

biophysical modelingprotein folding & dynamics

𝕏 PostBluesky

BiophysicsJournal of Chemical Information and ModelingPeer-reviewedJan 7, 2025

Enhanced Sampling Simulations of RNA-peptide Binding using Deep Learning Collective Variables

Nisha Kumari, Sonam Sonam, Tarak Karmakar

This study uses DeepTDA to design collective variables for enhanced sampling simulations of RNA-peptide binding, revealing multiple binding and unbinding events and calculating the free energy surface.

12 citations

protein structureprotein sequence

𝕏 PostBluesky