Publications — Anupam Anand Ojha

First-Author Publications 11

bioRxiv

cryoWEight: Conformational ensembles from cryo-EM particle images with weighted ensemble simulations

Anupam Ojha, Praveen Ranganath Prabhakar, Ioan Andricioaei, and Sonya Hanson

bioRxiv · Cold Spring Harbor Laboratory October 2026

10.64898/2026.09.28.755042

bioRxiv

PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants

Anupam Ojha, Gary Huber, Shiksha Dutta, and Sonya Hanson

bioRxiv · Cold Spring Harbor Laboratory September 2026

10.64898/2026.09.28.754770

ACS

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, and Rommie Amaro

Journal of Chemical Theory and Computation · American Chemical Society June 2026

10.1021/acs.jctc.6c00659

IUCr

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, and Sonya Hanson

Acta Crystallographica Section D · International Union of Crystallography March 2025

10.1107/S2059798325001469

ACS

Advances and challenges in milestoning simulations for drug-target kinetics

Anupam Ojha, Lane Votapka, and Rommie Amaro

Journal of Chemical Theory and Computation · American Chemical Society November 2024

Graphical abstract: Advances and challenges in milestoning simulations

10.1021/acs.jctc.4c01108

LiveCoMS

An introductory tutorial to the SEEKR2 multiscale milestoning software [article v1.0]

Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao, and Rommie Amaro

Living Journal of Computational Molecular Science January 2024

10.33011/livecoms.5.1.2359

RSC

QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Anupam Ojha, Lane Votapka, and Rommie Amaro

Chemical Science · Royal Society of Chemistry October 2023

10.1039/D3SC04195F

ACS

Selectivity and rank ordering of tight-binding JAK-STAT pathway inhibitors using Markovian milestoning with Voronoi tessellation simulations

Anupam Ojha, Ambuj Srivastava, Lane Votapka, and Rommie Amaro

Journal of Chemical Information and Modeling · American Chemical Society April 2023

10.1021/acs.jcim.2c01589

ACS

DeepWEST: Deep learning of kinetic models with the weighted ensemble simulation toolkit for enhanced sampling

Anupam Ojha, Saumya Thakur, Surl-Hee Ahn, and Rommie Amaro

Journal of Chemical Theory and Computation · American Chemical Society January 2023

10.1021/acs.jctc.2c00282

ACS

Gaussian-accelerated molecular dynamics with the weighted ensemble method: A hybrid method improves thermodynamic and kinetic sampling

Anupam Ojha†, Surl-Hee Ahn†, Rommie Amaro, and J. Andrew McCammon († equal contribution)

Journal of Chemical Theory and Computation · American Chemical Society November 2021

10.1021/acs.jctc.1c00770

MDPI

Molecular properties of drugs handled by kidney OATs and liver OATPs revealed by chemoinformatics and machine learning

Anupam Ojha†, Anisha Nigam†, Julia Li, Da Shi, Vibha Bhatnagar, Kabir Nigam, Ruben Abagyan, and Sanjay Nigam († equal contribution)

Pharmaceutics · Multidisciplinary Digital Publishing Institute October 2021

10.3390/pharmaceutics13101720

Co-Author Publications 13

ACS

Reconsidering excellence in the chemical sciences: Lessons from first-generation chemists

Robert A. Ives, David N. Azulay, Adam Cook, Mamta Dagar, Douglas J. Fansher, Roshan Keshari, Anupam Anand Ojha, Shivani Patel, Christian Sandoval-Pauker, Nitesh Sanghai, Brittany Trinh, Vishal Yadav, and Zhiling Zheng

ACS Central Science · American Chemical Society September 2026

10.1021/acscentsci.6c00822

bioRxiv

Deep learning-based modeling enhances efficacy of natural ligand CAR binders targeting CD70

Amrik Kang, Radhika Dalal, Mingcheng Li, Anupam Ojha, ..., Sonya Hanson, Pilar Cossio, Tanja Kortemme, Justin Eyquem, and Arun Wiita

bioRxiv · Cold Spring Harbor Laboratory September 2026

10.64898/2026.09.06.749651

APS

The Denario project: deep knowledge artificial intelligence agents for scientific discovery

Francisco Villaescusa-Navarro, Boris Bolliet, Pablo Villanueva-Domingo, Adrian E. Bayer, Aidan Acquah, Chetana Amancharla, Almog Barzilay-Siegal, Pablo Bermejo, Camille Bilodeau, Pablo Cárdenas Ramírez, Miles Cranmer, Urbano L. França, ChangHoon Hahn, Yan-Fei Jiang, Raul Jimenez, Jun-Young Lee, Antonio Lerario, Osman Mamun, Thomas Meier, Anupam A. Ojha, Pavlos Protopapas, Shimanto Roy, David N. Spergel, Pedro Tarancón-Álvarez, Ujjwal Tiwari, Matteo Viel, Digvijay Wadekar, Chi Wang, Bonny Y. Wang, Licong Xu, Yossi Yovel, Shuwen Yue, Wen-Han Zhou, Qiyao Zhu, Jiajun Zou, Íñigo Zubeldia

PRX Intelligence · American Physical Society October 2026

10.1103/kk55-gc95

In Revision

BCR::ABL1 mutations primarily confer resistance to asciminib and TGRX-678 by disrupting allosteric inhibition

Ariel Leyte-Vidal, Brian Farrell, Ian R. Outhwaite, Anupam Anand Ojha, Kallie M. Zuidema, Ailin Alvarez, Kaeli Miller, Carlynn Leavitt, Nellie Ahmadieh, Emma Gebauer, Vanie Seecharan, Isabelle Kwan, Ralf Landgraf, Kevin Lou, Muneeza Maqsood, Susan Branford, David Yeung, Timothy Hughes, Vivian G. Oehler, Delphine Rea, Kevan Shokat, Ivet Bahar, Eric S. Underbakke, Sonya Hanson, Markus A. Seeliger, and Neil P. Shah

In RevisionBlood · American Society of Hematology

Elsevier

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

Coordination Chemistry Reviews · ElsevierSubmitted

ACS

Prediction of threonine-tyrosine kinase receptor–ligand unbinding kinetics with multiscale milestoning and metadynamics

Lane Votapka, Anupam Ojha, Naoya Asada, and Rommie Amaro

Journal of Physical Chemistry Letters · American Chemical Society October 2024

10.1021/acs.jpclett.4c02332

Nature

Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens

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 August 2024