Related Experiment Video
Updated: Jul 6, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
Predicting binding motifs of complex adsorbates using machine learning with a physics-inspired graph representation
Wenbin Xu1,2, Karsten Reuter2, Mie Andersen3,4
1Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany.
Abstract:
Computational screening in heterogeneous catalysis relies increasingly on machine learning models for predicting key input parameters due to the high cost of computing these directly using first-principles methods. This becomes especially relevant when considering complex materials spaces such as alloys, or complex reaction mechanisms with adsorbates that may exhibit bi- or higher-dentate adsorption motifs. Here we present a data-efficient approach to the prediction of binding motifs and associated adsorption enthalpies of complex adsorbates at transition metals and their alloys based on a customized Wasserstein Weisfeiler-Lehman graph kernel and Gaussian process regression. The model shows good predictive performance, not only for the elemental transition metals on which it was trained, but also for an alloy based on these transition metals. Furthermore, incorporation of minimal new training data allows for predicting an out-of-domain transition metal. We believe the model may be useful in active learning approaches, for which we present an ensemble uncertainty estimation approach.
More Related Videos
10:21Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
Published on: February 23, 2024
09:17Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-protein Interfaces
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
The Equilibrium Binding Constant and Binding Strength
Molecular Models