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Dominic Rufa
Dominic Rufa
SandboxAQ
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Title
Cited by
Cited by
Year
SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids
J Jansen, KC Reimer, JS Nagai, FS Varghese, GJ Overheul, M de Beer, ...
Cell stem cell 29 (2), 217-231. e8, 2022
2122022
Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning/molecular mechanics potentials
DA Rufa, HE Bruce Macdonald, J Fass, M Wieder, PB Grinaway, ...
BioRxiv, 2020.07. 29.227959, 2020
862020
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
ML Boby, D Fearon, M Ferla, M Filep, L Koekemoer, MC Robinson, ...
Science 382 (6671), eabo7201, 2023
682023
COVID moonshot: open science discovery of SARS-CoV-2 main protease inhibitors by combining crowdsourcing, high-throughput experiments, computational simulations, and machine …
H Achdout, A Aimon, E Bar-David, GM Morris
BioRxiv, 2020
552020
End-to-end differentiable construction of molecular mechanics force fields
Y Wang, J Fass, B Kaminow, JE Herr, D Rufa, I Zhang, I Pulido, M Henry, ...
Chemical Science 13 (41), 12016-12033, 2022
462022
Tuning the Baird aromatic triplet-state energy of cyclooctatetraene to maximize the self-healing mechanism in organic fluorophores
AK Pati, O El Bakouri, S Jockusch, Z Zhou, RB Altman, GA Fitzgerald, ...
Proceedings of the National Academy of Sciences 117 (39), 24305-24315, 2020
442020
Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors
COVID Moonshot Consortium, H Achdout, A Aimon, DS Alonzi, R Arbon, ...
BioRxiv, 2020.10. 29.339317, 2020
402020
End-to-end differentiable molecular mechanics force field construction
Y Wang, J Fass, B Kaminow, JE Herr, D Rufa, I Zhang, I Pulido, M Henry, ...
arXiv preprint arXiv:2010.01196, 2020
182020
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein: protein complex
I Zhang, DA Rufa, I Pulido, MM Henry, LE Rosen, K Hauser, S Singh, ...
Journal of chemical theory and computation 19 (15), 4863-4882, 2023
122023
Perses
DA Rufa, I Zhang, HE Bruce Macdonald, PB Grinaway, I Pulido, ...
Please cite this software using these metadata, 2022
32022
Fine-tuning molecular mechanics force fields to experimental free energy measurements
D Rufa, J Fass, JD Chodera
bioRxiv, 2025.01. 06.631610, 2025
2025
Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein: Protein Complex
I Zhang, DA Rufa, I Pulido, MM Henry, LE Rosen, K Hauser, S Singh, ...
Journal of Chemical Theory and Computation 20 (2), 990-991, 2024
2024
2017 T Division Lightning Talks
ML Ramsey, JAMM Abeywardhana, CM Adams, LC Adams, AL Carter, ...
Los Alamos National Lab.(LANL), Los Alamos, NM (United States), 2017
2017
Adaptive sampling for alchemical free energy calculations and applications for drug design
HE Bruce Macdonald, DA Rufa, PB Grinaway, JD Chodera
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Articles 1–14