no code implementations • 16 Oct 2023 • Jenna C. Fromer, David E. Graff, Connor W. Coley
The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem.
no code implementations • 14 May 2023 • David E. Graff, Edward O. Pyzer-Knapp, Kirk E. Jordan, Eugene I. Shakhnovich, Connor W. Coley
When the correlation between structure and property weakens, a dataset is described as "rough," but this characteristic is partly a function of the chosen representation.
2 code implementations • 19 Jul 2022 • Matteo Aldeghi, David E. Graff, Nathan Frey, Joseph A. Morrone, Edward O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley
In molecular discovery and drug design, structure-property relationships and activity landscapes are often qualitatively or quantitatively analyzed to guide the navigation of chemical space.
2 code implementations • 3 May 2022 • David E. Graff, Matteo Aldeghi, Joseph A. Morrone, Kirk E. Jordan, Edward O. Pyzer-Knapp, Connor W. Coley
In this study, we propose an extension to the framework of model-guided optimization that mitigates inferences costs using a technique we refer to as design space pruning (DSP), which irreversibly removes poor-performing candidates from consideration.
1 code implementation • 17 Dec 2021 • David E. Graff, Connor W. Coley
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking.
1 code implementation • 13 Dec 2020 • David E. Graff, Eugene I. Shakhnovich, Connor W. Coley
Structure-based virtual screening is an important tool in early stage drug discovery that scores the interactions between a target protein and candidate ligands.