Computational Drug Repurposing with Multiscale Interactomes
A step-by-step workflow to identify repurposing candidates by integrating heterogeneous biomedical networks, graph embeddings, and experimental prioritization.
Apr 23, 2024
How to Validate AlphaFold Structures
Practical guide to checking AlphaFold-predicted protein models using pLDDT, PAE, geometry validation tools, structural comparisons, and functional tests.
Mar 28, 2024
EnsembleBBB
Feb 19, 2024
Interpretable Machine Learning as a Key to Understanding BBB Permeability
Step-by-step tutorial on building an explainable ML model to predict blood-brain barrier permeability, using feature importance and SHAP analysis for interpretability.
Jan 23, 2024
How to build and validate 3D-QSAR models - Insights from Xu et al., 2020
Comprehensive, metric-driven workflow for robust 3D-QSAR modeling, based on Xu et al., 2020 and enriched with cheminformatics best practices.
Jan 13, 2024
Data-Driven Chemistry: How Data Science Empowers Drug Discovery
Exploring how data science techniques—from machine learning to data visualization—are transforming chemistry and accelerating the discovery of new drugs and materials.
Nov 8, 2023
Using PaDELPy to Generate Molecular Fingerprints for Machine Learning-Based QSAR
A step-by-step tutorial on using PaDELPy to calculate molecular fingerprints and build a Random Forest model for predicting molecular activity in drug discovery.
Mar 15, 2023
How Long Should Molecular Dynamics Simulations Run? A Practical Guide
Guidelines for choosing appropriate MD simulation lengths in protein–ligand systems, with key convergence metrics like RMSD, RMSF, and interaction fingerprints.
Jan 9, 2023
Chemical Databases Every ML Scientist Should Know for Drug Discovery
Overview of freely available chemical and bioactivity databases—including ChEMBL, BindingDB, PubChem, PDBbind, and BRENDA—that fuel machine learning and cheminformatics research in drug discovery.
Sep 12, 2022
How to Perform Data Curation and Classify Bioactivity Data on ChEMBL Database
Step-by-step tutorial on retrieving, curating, and classifying ChEMBL bioactivity data for machine learning applications in drug discovery.
Sep 7, 2022