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First-Author Publications 11
In Preparation
PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants
Anupam Ojha
In PreparationApril 2026
Graphical abstract
In Preparation
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 PreparationApril 2026
Graphical abstract
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 · Cold Spring Harbor Laboratory July 2025
Graphical abstract: seekrflow 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 Crystallographica Section D · International Union of Crystallography March 2025
Graphical abstract 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
Graphical abstract 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
Graphical abstract: QMrebind 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
Graphical abstract 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
Graphical abstract 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
Graphical abstract 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
Graphical abstract 10.3390/pharmaceutics13101720
Co-Author Publications 12
In Preparation
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 PreparationApril 2026
Graphical abstract
In Preparation
Considering 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 Zhang
In PreparationApril 2026
Graphical abstract
arXiv
The Denario project: deep knowledge AI 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
arXiv · Cornell University October 2025
Graphical abstract 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
Coordination Chemistry Reviews · ElsevierSubmitted · September 2025
Graphical abstract
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
Graphical abstract 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
Graphical abstract 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 · Multidisciplinary Digital Publishing Institute April 2024
Graphical abstract 10.3390/pharmaceutics16050592
ACS
SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine
Lane Votapka, Andrew Stokely, Anupam Ojha, and Rommie Amaro
Journal of Chemical Information and Modeling · American Chemical Society June 2022
Graphical abstract 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
Journal of Chemical Theory and Computation · American Chemical Society June 2020
Graphical abstract 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 Part A · Elsevier June 2019
Graphical abstract 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 · American Chemical Society July 2018
Graphical abstract 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 · American Chemical Society May 2017
Graphical abstract 10.1021/acs.inorgchem.7b00787