Workflow library
- OpenADMET CYP3A4 Inhibition Models (CPU) - Trains and cross-validates four tree models (LightGBM, random forest, XGBoost, CatBoost) on the ChEMBL35 CYP3A4 IC50 data with openadmet-models v0.2.0. It compares the models statistically and uses the best one (highest mean CV R2) to predict CYP3A4 inhibition (pIC50) for a list of compounds. Runs on CPU only. Input: a CSV of compounds with an OPENADMET_CANONICAL_SMILES column. Outputs: CV metrics per model, comparison plots, predictions for every compound and the top 50 predicted inhibitors. Port of the OpenADMET Showcase (OpenADMET/openadmet-demos, Apache-2.0).
- Lacuna + AutoDock Vina Docking - Find cryptic binding pockets that are invisible in a single static structure and then dock them using AutoDock Vina.
- Lacuna Cryptic Pocket Discovery - Find cryptic binding pockets that are invisible in a single static structure using Lacuna in Horus.
- AutoDock Vina Docking - AutoDock Vina with preparation steps. Changelog: - Updated input variables to support center and box size.
- Boltz2 Virtual Screening - W-01 · Boltz-2 Virtual Screening
- BioExcel Membrane MD Analysis - GABA-gated Chloride Channel (A023K) - W-26 · Protein-Membrane MD Analysis
- BioExcel Autoencoder - MD Trajectory Analysis with Machine Learning - W-25 · AutoEncoders for MD Analysis
- BioExcel HADDOCK Antibody-Antigen Protein-Protein Docking - W-24 · HADDOCK3 Protein-Protein Docking
- BioExcel Structure Checking - 1Z83 (AK1A) - W-23 · Molecular Structure Checking
- BioExcel CMIP - Classical Molecular Interaction Potentials - W-22 · Classical Molecular Interaction Potentials
- BioExcel FlexServ - Protein Conformational Dynamics (1A32) - W-21 · Macromolecular Coarse-Grained Flexibility
- BioExcel GoDMD - Adenylate Kinase Conformational Transition - W-20 · Protein Conformational Transitions
- BioExcel FlexDyn - Protein Flexibility and Dynamics Analysis - W-19 · Protein Conformational Ensembles
- BioExcel AMBER ABC Setup - Drew-Dickerson Dodecamer DNA - W-18 · ABC MD Setup
- BioExcel DNA Helical Parameters Analysis - W-17 · DNA Helical Parameters
- BioExcel AMBER Constant pH MD Setup - BPTI 6PTI - W-16 · AMBER Constant pH MD Setup
- BioExcel AMBER MD Setup - Protein-Ligand Complex (T4 Lysozyme 3HTB + JZ4) - W-15 · AMBER Protein-Ligand Complex MD Setup
- BioExcel Virtual Screening - Protein-Ligand Docking with fpocket (p38α / Imatinib) - W-13 · Protein-Ligand Docking (Fpocket Binding Site)
- Virtual Screening - Protein-Ligand Docking via EBI PDBe API (p38-alpha / Dasatinib) - W-12 · Protein-Ligand Docking (PDBe REST-API Binding Site)
- BioExcel Virtual Screening - Protein-Ligand Docking - Cluster90 Binding Site - W-11 · Protein-Ligand Docking (PDB Cluster90 Binding Site)
- PMX Mutation Free Energy Calculations - Staphylococcal nuclease I10A - W-10 · Mutation Free Energy Calculations
- BioExcel MD Setup - Protein-Ligand Complex (3HTB + JZ4) - W-09 · GROMACS Protein-Ligand Complex MD Setup
- BioExcel AMBER MD Setup - Lysozyme 1AKI - W-05 · AMBER MD Setup
- BioExcel Ligand Parameterization - W-04 · Ligand Parameterization
- BioExcel MD Setup - Lysozyme 1AKI - W-03 · GROMACS MD Setup