Drug Discovery

A Jupyter Notebook pipeline for building QSAR classification models for bioactivity prediction, supporting descriptor calculation, feature selection, model training, and applicability domain assessment.

Feb 20, 2024

A machine learning ensemble for predicting drug blood-brain barrier permeability. The models, fingerprints, and prediction script are in the GitHub repository. The hosted Streamlit app currently asks visitors to sign in, so the repository is the public entry point.

Feb 13, 2024

Practical introduction to DataWarrior as a free, chemistry-aware workbench for data visualization, filtering, and focused library generation, based on Bruno Villoutreix’s tutorial series.

Feb 7, 2024

A curated resource list of computational methods for drug discovery, covering molecular modeling tools, machine learning frameworks, databases, and open-source pipelines organized by application area.

Jan 16, 2024

Step-by-step workflow for performing PCA and Free Energy Landscape (FEL) analysis from MD simulations with GROMACS.

Nov 22, 2023

Learn how to use Density Functional Theory (DFT) to validate docking poses, estimate strain energies, and gain quantum insights into ligand binding.

Oct 27, 2023

Step-by-step guide to constructing an open-source drug discovery pipeline with AI and chemistry tools, from data to visualization.

Oct 1, 2023

Overview of key molecular simulation methods (QM, MD, CGMD, MC, BD, LD, DPD) and their strategic applications in drug discovery pipelines.

Aug 10, 2023

Practical guide to checking AlphaFold-predicted protein models using pLDDT, PAE, geometry validation tools, structural comparisons, and functional tests.

Jun 19, 2023

A random forest on the B3DB blood-brain barrier set, scored on a held-out split, then opened with impurity importance and SHAP. TopoPSA is in the descriptor block only if you select that block on purpose.

May 24, 2023