Flatiron Institute · Simons Foundation · New York
Anupam Anand Ojha, Ph.D.
Flatiron Research Fellow  ·  Center for Computational Biology & Center for Computational Mathematics  ·  Flatiron Institute, New York, NY, USA
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, and DeepWEST.

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, MolSSI SEED Fellowship, Distinguished Graduate Student Fellowship, Merkin Graduate Fellowship, Merck Research Award for Underrepresented Chemists of Color, and the Flatiron Research Fellowship, among others.

Beyond research, Dr. Ojha is committed to equity, diversity, and inclusion, having served in leadership roles including the UC San Diego Academic Senate Committee, Chemistry International Friendship Group, and Chemistry Graduate Student Council.

Latest Publications
01 · July 2025
seekrflow: Towards an end-to-end automated simulation pipeline with machine-learned force field for accelerated drug-target kinetic and thermodynamic predictions
Anupam Ojha, Lane Votapka, Shiksha Dutta, Anson Noland, Sonya Hanson, Rommie Amaro
bioRxiv
02 · March 2025
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation
Anupam Ojha, Robert Blackwell, Eduardo Cruz-Chú, Raison Dsouza, Miro Astore, Peter Schwander, Sonya Hanson
Acta Cryst. D
03 · November 2024
Advances and challenges in milestoning simulations for drug-target kinetics
Anupam Ojha, Lane Votapka, Rommie Amaro
JCTC · ACS
04 · August 2024
Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens
Xandra Nuqui, Lorenzo Casalino, …, Anupam Ojha, …, Rommie Amaro
Nature Comms.
View all 22 publications →