About Me

I am a computational biologist and AI researcher, currently focused on protein design and nucleic acid interactions. I completed my PhD in Computational Biology and Bioinformatics, at the University of Southern California in 2024, where I developed geometric deep learning methods to predict protein-DNA binding specificity, visualize RNA 3D structures, and build interactive databases for protein-DNA and protein-RNA complexes. My undergraduate education was in Computer Science and Engineering from IIT Kanpur.

Currently, I am a postdoctoral scholar at the University of Washington, applying generative modeling and AI-driven approaches, including RFdiffusion3, to design all-atom biomolecular interactions, optimize protein and NA sequences, and design nucleic acid binding proteins (e.g., transcription factors). My work combines deep learning, structural bioinformatics, and protein-nucleic acid modeling to develop data-driven tools for biomolecular design.

I have contributed to multiple open-access resources, including Atomworks, RFDiffusion3, DeepPBS, DNAproDB and RNAproDB, and have presented my research at leading institutions and conferences worldwide. I am passionate about creating accessible computational tools that bridge AI and molecular biology to advance rational biomolecular design.

Current Position

Postdoctoral scholar, Institute for Protein Design (Baker Lab), University of Washington, 2025-present

Socials

📝 Publications

1. Geometric deep learning of protein-DNA binding specificity
   Nature Methods, 21(9), 1674–1683, Aug 2024 (webserver)
   Raktim Mitra, Jinsen Li, Jared M. Sagendorf, Yibei Jiang, Ari S. Cohen, Tsu-Pei Chiu, Cameron J. Glasscock, Remo Rohs

2. De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
   BioRxiv, preprint, Sept 2025, UW
   Jasper Butcher*, Rohith Krishna*, Raktim Mitra*, Rafael I. Brent*, Yanjing Li*, Nathaniel Corley*, …, David Baker

3. RVAgene: Generative modeling of gene expression timeseries data
   Bioinformatics, 37(19), 3252–3262, Oct 2021, USC
   Raktim Mitra, Adam L. MacLean

4. DNAproDB: An updated database for the automated and interactive analysis of protein–DNA complexes
   Nucleic Acids Research, 53(D1), D396–D402, Jan 2025, USC (webserver)
   Raktim Mitra*, Ari S. Cohen*, Jared M. Sagendorf, Helen M. Berman, Remo Rohs

5. RNAproDB: A Webserver and Interactive Database for Analyzing Protein–RNA Interactions
   Journal of Molecular Biology, in press, Jan 2025, USC (webserver)
   Raktim Mitra*, Ari S. Cohen*, Wei Yu Tang*, Hirad Hosseini, Yongchan Hong, Helen M. Berman, Remo Rohs

6. RNAscape: Geometric mapping and customizable visualization of RNA structure
   Nucleic Acids Research, 52(W1), W354–W361, Mar 2024, USC (webserver)
   Raktim Mitra*, Ari S. Cohen*, Remo Rohs

7. Accelerating Biomolecular Modeling with AtomWorks and RF3
   BioRxiv, preprint, Aug 2025, UW
   Nathaniel Corley, Simon Mathis, Rohith Krishna, …, Raktim Mitra, …, David Baker, Frank DiMaio

8. RNA sequence design and protein–DNA specificity prediction with NA-MPNN
   BioRxiv, preprint, Oct 2025, UW
   Andrew Kubaney, Andrew H. Favor, Lilian McHugh, Raktim Mitra, Robert Pecoraro, Justas Dauparas, Cameron Glasscock, David Baker

9. Novel fold and wing structure of Forkhead TF facilitate DNA binding
   Nucleic Acids Research, 53(18), Oct 2025, USC
   George L. Wang, Yibei Jiang, Yuying Sun, Fariborz Nasertorabi, Jesse A. Weller, Raktim Mitra, Alexander Batyuk, Oscar M. Aparicio, Vadim Cherezov, Remo Rohs

10. Structure-based prediction of protein-nucleic acid binding using graph neural networks (PNAbind)
    Biophysical Reviews, 16(3), 297–314, June 2024, USC
    Jared M. Sagendorf, Raktim Mitra, Jiawei Huang, Xiaojiang S. Chen, Remo Rohs

11. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox–DNA binding
    Biophysical Journal, 123(2), 248–259, Jan 2024, USC
    Yibei Jiang, Tsu-Pei Chiu, Raktim Mitra, Remo Rohs

12. Tejaas: reverse regression increases power for detecting trans-eQTLs
    Genome Biology, 22(1), Article 142, May 2021, MPIMS
    Saikat Banerjee, Franco L. Simonetti, Kira E. Detrois, Anubhav Kaphle, Raktim Mitra, Rahul Nagial, Johannes Söding