CV
John E. Herr
Education
University of Notre Dame
Ph.D. Theoretical and Computational Chemistry (August 2015 - May 2020)
University of Iowa
B.S. Chemistry and Mathematics (August 2011 - May 2014)
Southeastern Community College
Associate of Arts (August 2007 - July 2010)
Research Experience
Postdoctoral Research Assistant, Dr. John Chodera
September 2021 - June 2022
- Designed drug-like molecule datasets for training neural network force fields.
- Trained transformer neural network models for molecular energy, atomic forces, and partial charges.
Postdoctoral & Graduate Research Assistant, Drs. Olaf Wiest and Paul Helquist
May 2020 - October 2020; August 2018 - May 2020
- Implemented graph neural network code in PyTorch for reaction product prediction.
- Extended models to include reaction yield data from pharmaceutical datasets.
Graduate Research Assistant, Dr. John Parkhill
August 2015 - August 2018
- Developed datasets for training neural network force fields.
- Trained neural network models for molecular properties using TensorFlow.
Publications
Spice: A dataset of drug-like molecules and peptides for ML potentials
Scientific Data, 10, 11 (2023)
DOI:10.1038/s41597-022-01882-6On the use of real-world datasets for reaction yield prediction
Chemical Science, 14, 4997–5005 (2023)
DOI:10.1039/D2SC06041HEnd-to-end differentiable construction of molecular mechanics force fields
Chemical Science, 13, 12016–12033 (2022)
DOI:10.1039/D2SC02739A
For a full list of publications, visit my Google Scholar
Technical Skills
- Python
- PyTorch, TensorFlow, Scikit-Learn, RDKit
- Git
- Linux
- Computational chemistry software packages
- Q-Chem, ORCA, CP2K, VASP