Dirac--Bianconi Graph Neural Networks -- Enabling Non-Diffusive Long-Range Graph Predictions

1 code implementation • 17 Jul 2024 • Christian Nauck, Rohan Gorantla, Michael Lindner, Konstantin Schürholt, Antonia S. J. S. Mey, Frank Hellmann

The geometry of a graph is encoded in dynamical processes on the graph.

Graph Neural Network

SILVR: Guided Diffusion for Molecule Generation

1 code implementation • 21 Apr 2023 • Nicholas T. Runcie, Antonia S. J. S. Mey

Computationally generating novel synthetically accessible compounds with high affinity and low toxicity is a great challenge in drug design.

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks

2 code implementations • 13 May 2021 • David F. Hahn, Christopher I. Bayly, Hannah E. Bruce Macdonald, John D. Chodera, Vytautas Gapsys, Antonia S. J. S. Mey, David L. Mobley, Laura Perez Benito, Christina E. M. Schindler, Gary Tresadern, Gregory L. Warren

Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs.

Benchmarking Drug Discovery

Best Practices for Alchemical Free Energy Calculations

1 code implementation • 7 Aug 2020 • Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald, John D. Chodera, Maximilian Kuhn, Julien Michel, David L. Mobley, Levi N. Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R. Shirts, Gary Tresadern, Huafeng Xu

Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another.