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

I am a Flatiron Research Fellow at the Flatiron Institute (Simons Foundation), New York, working at the intersection of multiscale simulation, cryo-EM, and machine learning to accelerate drug discovery.

I received my Ph.D. in Chemistry from UC San Diego in 2024, advised by Prof. Rommie E. Amaro and Prof. J. Andrew McCammon. My current tools — seekrflow, cryoWEight, and ManifoldEM — bridge molecular dynamics, cryo-EM, and deep learning.

I am an NSF I-Corps Fellow, CAS Future Leader, and AI 2030 Global Fellow.

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 →