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First-Author Publications 11
In Prep
PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants
Anupam Ojha
In PreparationJan. 2026
In Prep
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
In PreparationJan. 2026
bioRxiv
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
bioRxiv bioRxiv · Cold Spring Harbor Laboratory · July 2025 10.1101/2025.08.13.669965
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 Cryst. D Acta Crystallographica Section D · International Union of Crystallography · Mar. 2025 10.1107/S2059798325001469
ACS
Advances and challenges in milestoning simulations for drug-target kinetics
Anupam Ojha, Lane Votapka, and Rommie Amaro
JCTC · ACS Journal of Chemical Theory and Computation · American Chemical Society · Nov. 2024 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
LiveCoMS Living Journal of Computational Molecular Science · Jan. 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 · RSC Chemical Science · Royal Society of Chemistry · Oct. 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
JCIM · ACS Journal of Chemical Information and Modeling · American Chemical Society · Apr. 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
JCTC · ACS Journal of Chemical Theory and Computation · American Chemical Society · Jan. 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)
JCTC · ACS Journal of Chemical Theory and Computation · American Chemical Society · Nov. 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 · MDPI Pharmaceutics · MDPI · Oct. 2021 10.3390/pharmaceutics13101720
Co-Author Publications 11
In Prep
Deep learning algorithms identify CD27 mutations with improved predicted CD70 binding
Amrik Kang, Anupam Ojha, Radhika Dalal, Sonya Hanson, Pilar Cossio, and Arun Wiita
In PreparationJan. 2026
arXiv
The Denario project: Deep knowledge AI agents for scientific discovery
Francisco Villaescusa-Navarro, Boris Bolliet, …, Anupam A. Ojha, … et al.
arXiv arXiv · Cornell University · Oct. 2025 10.48550/arXiv.2510.26887
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
SubmittedCoordination Chemistry Reviews · Elsevier · Sept. 2025
ACS
Prediction of Threonine-Tyrosine Kinase Receptor–Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics
Lane Votapka, Anupam Ojha, Naoya Asada, and Rommie Amaro
JPCL · ACS Journal of Physical Chemistry Letters · American Chemical Society · Oct. 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 Tse, Anupam Ojha, Fiona Kearns, Mia Rosenfeld, Emily Miller, Cory Acreman, Surl-Hee Ahn, Kartik Chandran, Jason McLellan, and Rommie Amaro
Nature Communications Nature Communications · Springer Nature · Aug. 2024 10.1038/s41467-024-50976-9
MDPI
Distinguishing Molecular Properties of OAT, OATP, and MRP Drug Substrates by Machine Learning
Anisha Nigam, Jeremiah D. Momper, Anupam Ojha, and Sanjay Nigam
Pharmaceutics · MDPI Pharmaceutics · MDPI · Apr. 2024 10.3390/pharmaceutics16050592
ACS
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine
Lane Votapka, Andrew Stokely, Anupam Ojha, and Rommie Amaro
JCIM · ACS Journal of Chemical Information and Modeling · American Chemical Society · June 2022 10.1021/acs.jcim.2c00501
ACS
Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach
Benjamin Jagger, Anupam Ojha, and Rommie Amaro
JCTC · ACS Journal of Chemical Theory and Computation · American Chemical Society · June 2020 10.1021/acs.jctc.0c00495
Elsevier
Paper based field deployable sensor for naked eye monitoring of copper (II) ions; elucidation of binding mechanism by DFT studies
Halali Vishaka, Manav Saxena, H. R. Chandan, Anupam Ojha, and R. Geetha Balakrishna
Spectrochimica Acta A · Elsevier Spectrochimica Acta Part A · Elsevier · June 2019 10.1016/j.saa.2019.117291
ACS
Water-Stable Nanoscale Zirconium-Based Metal-Organic Frameworks for the Effective Removal of Glyphosate from Aqueous Media
Asha Pankajakshan, Mekhola Sinha, Anupam Ojha, and Sukhendu Mandal
ACS Omega ACS Omega · American Chemical Society · July 2018 10.1021/acsomega.8b00921
ACS
Turn-on Fluorescence Sensing and Discriminative Detection of Aliphatic Amines Using a 5-Fold-Interpenetrated Coordination Polymer
Prabu Mani, Anupam Ojha, Vennapusa Reddy, and Sukhendu Mandal
Inorganic Chemistry · ACS Inorganic Chemistry · American Chemical Society · May 2017 10.1021/acs.inorgchem.7b00787