no code implementations • 28 Jun 2022 • Yanwu Xu, Shaoan Xie, Maxwell Reynolds, Matthew Ragoza, Mingming Gong, Kayhan Batmanghelich
An organ segmentation method that can generalize to unseen contrasts and scanner settings can significantly reduce the need for retraining of deep learning models.
2 code implementations • 28 Oct 2021 • Matthew Ragoza, Tomohide Masuda, David Ryan Koes
The goal of structure-based drug discovery is to find small molecules that bind to a given target protein.
1 code implementation • 17 Oct 2020 • Matthew Ragoza, Tomohide Masuda, David Ryan Koes
Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models.
1 code implementation • 16 Oct 2020 • Tomohide Masuda, Matthew Ragoza, David Ryan Koes
We show that valid and unique molecules can be readily sampled from the variational latent space defined by a reference `seed' structure and generated structures have reasonable interactions with the binding site.
1 code implementation • 6 Mar 2018 • Joshua Hochuli, Alec Helbling, Tamar Skaist, Matthew Ragoza, David Ryan Koes
Here we present three methods for visualizing how individual protein-ligand complexes are interpreted by 3D convolutional neural networks.
1 code implementation • 20 Oct 2017 • Matthew Ragoza, Lillian Turner, David Ryan Koes
Docking is an important tool in computational drug discovery that aims to predict the binding pose of a ligand to a target protein through a combination of pose scoring and optimization.
2 code implementations • 8 Dec 2016 • Matthew Ragoza, Joshua Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes
A CNN scoring function automatically learns the key features of protein-ligand interactions that correlate with binding.