Related Experiment Video
Updated: Jan 6, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Extremely Randomized Trees to Determine Binding Affinity
Amauri Duarte da Silva1, Walter Filgueira de Azevedo2
1Graduate Program in Information Technologies and Health Management, Federal University of Health Sciences of Porto Alegre, Porto Alegre, RS, Brazil.
Abstract:
Merging artificial intelligence and computational systems biology has the potential to address complex systems with a holistic view. This integration allows us to build robust regression models to predict enzyme inhibition using data obtained from docking simulations. This work adopts a hands-on approach to generate regression models to predict the inhibition of cyclin-dependent kinase 2. This protein is an anticancer drug target, and we have data for crystallographic structures and inhibition of this enzyme. We employed the Extremely Randomized Trees method implemented in the program SAnDReS 2.0 to predict CDK2 inhibition. Our regression models employ docking results obtained using protein-ligand docking programs Molegro Virtual Docker and AutoDock Vina 1.2. Our Extra Trees regression models showed superior performance compared with other machine learning techniques. All CDK2 datasets and a Jupyter Notebook with SKReg4Model discussed in this work are available at GitHub: https://github.com/azevedolab/docking#readme . We made the source code of the program SAnDReS 2.0 available at https://github.com/azevedolab/sandres .
More Related Videos
Related Concept Videos
The Equilibrium Binding Constant and Binding Strength
The Equilibrium Binding Constant and Binding Strength
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...
Structure-Activity Relationships and Drug Design
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
Protein-Drug Binding: Determination Methods
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
Ligand Binding and Linkage

