Flatiron Institute · Simons Foundation · New York
Anupam Anand Ojha
Anupam Anand Ojha, Ph.D.
Flatiron Research Fellow · Center for Computational Biology & Center for Computational Mathematics
Flatiron Institute, New York, United States
About

Anupam Anand Ojha is a Flatiron Research Fellow at the Center for Computational Biology and the Center for Computational Mathematics at the Flatiron Institute. He specializes in theoretical and computational biophysics, focusing on developing multiscale simulations at the intersection of cryo-electron microscopy, machine learning, and biomolecular modeling. His work aims to study protein-ligand and protein-protein interactions, model kinetic pathways involved in molecular recognition and signal transduction, and enhance understanding of complex biomolecular systems for accelerated drug discovery.

Dr. Ojha earned his Ph.D. in Chemistry with a specialization in Theoretical and Computational Biophysics from the University of California, San Diego, under the mentorship of Prof. Rommie E. Amaro and Prof. J. Andrew McCammon. During his doctoral research, he developed multiscale computational methods integrating Brownian dynamics, enhanced molecular dynamics, quantum mechanics, and machine learning approaches to advance drug discovery and deepen biomolecular understanding. He has made significant contributions to computational biophysics, including developing advanced algorithms and software packages such as SEEKR, QMrebind, GaMD-WE, DeepWEST, cryoWEight, ManifoldEM, seekrflow, and PySTARC.

His research achievements are complemented by a robust publication record featuring several first-author papers in prestigious journals and invitations to present at numerous international conferences. Dr. Ojha's excellence has been recognized through awards including the Swiss Government Excellence Scholarship, Molecular Sciences Software Institute SEED Fellowship, Distinguished Graduate Student Fellowship, Merkin Graduate Fellowship, Merck Research Award for Underrepresented Chemists of Color, and the Flatiron Research Fellowship, among others.

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Latest Publications
July 2025
Anupam Ojha, Lane Votapka, Shiksha Dutta, Anson Noland, Sonya Hanson, and Rommie Amaro
bioRxiv · Cold Spring Harbor Laboratory
March 2025
Anupam Ojha, Robert Blackwell, Eduardo Cruz-Chú, Raison Dsouza, Miro Astore, Peter Schwander, and Sonya Hanson
Acta Crystallographica Section D · International Union of Crystallography
November 2024
Anupam Ojha, Lane Votapka, and Rommie Amaro
Journal of Chemical Theory and Computation · American Chemical Society
August 2024
Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L. Tse, Anupam A. Ojha, Fiona L. Kearns, Mia A. Rosenfeld, Emily Happy Miller, Cory M. Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S. McLellan, and Rommie E. Amaro
Nature Communications · Springer Nature
Upcoming Publications
April 2026
PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants
Anupam Ojha
Submitted
April 2026
cryoWEight: An automated framework for iterative ensemble cryo-EM-guided reweighting for biomolecular complexes
Anupam Ojha, Praveen Ranganath Prabhakar, Ioan Andricioaei, Pilar Cossio, and Sonya Hanson
Submitted
April 2026
Deep learning algorithms identify CD27 mutations with improved predicted CD70 binding
Amrik Kang, Anupam Ojha, Radhika Dalal, Sonya Hanson, Pilar Cossio, and Arun Wiita
Submitted
April 2026
MXenes at the interface of biology and materials for biomedical applications
Mallamma Jinagi, Pallavi Jagdale, Sayali Patil, Sneha Mondal, Arvind Jadhav, Akshaya Samal, Mohit Saraf, Anupam Ojha, and Manav Saxena
Submitted
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