Open source

Workflow library

27 production-ready workflows for the horus-runtime engine. Each workflow runs a multi-stage pipeline. Each stage selects its own compute target: a local CPU, a remote GPU, a container, or an HPC scheduler. Horus moves the data across every boundary for you.

Looking for workflows published by other teams? Browse published workflows.

Drug discovery

Screen ligand libraries against a target. The GPU stages run remotely; the prep and ranking stages stay local.

AutoDock Vina Docking

Dock a whole ligand library into a receptor pocket with AutoDock Vina. Meeko and OpenBabel prepare the PDBQT inputs, and Horus routes the docking stage to the hardware you pick.

AutoDock VinaMeekoOpenBabelRDKit
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Boltz-2 Virtual Screening

Predict the binding structure and the affinity of every protein-ligand pair with Boltz-2, then rank the best candidates. The GPU stage runs remotely; the prep and ranking stages stay local.

Boltz-2CUDADockerSSH
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Molecular dynamics

Molecular dynamics setup and analysis built on the BioExcel building blocks. Each stage selects its own executor.

ABC DNA MD Setup

Run the Ascona B-DNA Consortium DNA setup protocol with AmberTools, LEaP, cpptraj and sander. Ten equilibration stages, hydrogen-mass repartitioning and a 4 fs production run.

AMBERAmberToolssandercpptraj
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AMBER Constant pH MD Setup

Run a constant pH molecular dynamics simulation with AmberTools and sander, then predict per-residue pKa values with cphstats. Horus routes each stage to its own executor.

AMBERAmberToolssanderLEaP
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AMBER MD Setup

Run a full AMBER molecular dynamics setup for lysozyme 1AKI with LEaP, sander, and cpptraj. Horus routes the ARM64-incompatible AmberTools stages to a Docker executor.

AMBERAmberToolssandercpptraj
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AMBER Protein MD Setup

Set up and run a full protein MD simulation with AmberTools, sander and cpptraj. Horus routes the AMBER stages to Docker and keeps the biobb Python stages in a native conda environment.

AMBERAmberToolssandercpptraj
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AMBER Protein-Ligand Complex MD Setup

Parameterize a ligand with ACPype and GAFF, build the complex topology with LEaP, then run the full sander MD protocol with AmberTools. Horus assigns an executor per stage.

AMBERAmberToolssandercpptraj
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AutoEncoders for MD Trajectory Analysis

Train a multilayer AutoEncoder on MD trajectory data with biobb_pytorch. Compare apo and holo latent spaces, check the reconstruction with RMSF, then export a PLUMED variable.

PyTorchBioExcel biobbPLUMEDGROMACS
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Classical Molecular Interaction Potentials with CMIP

Compute Classical Molecular Interaction Potentials with CMIP across three case studies: Lysozyme MIP grids, EGFR-Erlotinib protein-ligand energies, and RBD-hACE2 energies.

CMIPBioExcel biobbAMBERACPype
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DNA Helical Parameters Analysis

Extract helical parameters from a DNA MD trajectory with Curves+ and Canal, then fan out to averages, time series, stiffness, bimodality and correlations with biobb_dna.

Curves+Canalbiobb_dnaBioExcel biobb
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GROMACS MD Setup

Run a complete GROMACS molecular dynamics setup for lysozyme 1AKI with the CHARMM36 force field. Horus builds the conda environment and routes each stage to the right hardware.

GROMACSBioExcel biobbCHARMM36conda
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GROMACS Protein-Ligand Complex MD Setup

Build and simulate a protein-ligand complex in GROMACS. ACPype parameterizes the JZ4 ligand with GAFF, and the merged 3HTB complex runs through minimization, equilibration, and MD.

GROMACSACPypeGAFFOpenBabel
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HADDOCK3 Antibody-Antigen Protein-Protein Docking

Run an information-driven antibody-antigen docking protocol with HADDOCK3. Prepare both chains, build ambiguous interaction restraints, then dock, refine, cluster, and score with CAPRI.

HADDOCK3BioExcel biobbbiobb_pdb_toolsAmberTools
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Ligand Parameterization

Parameterize a small-molecule ligand with ACPype and the GAFF force field, then emit GROMACS topology files. OpenBabel adds and minimizes the hydrogens first.

ACPypeGAFFOpenBabelGROMACS
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Macromolecular Coarse-Grained Flexibility with FlexServ

Reproduce the FlexServ protocol for macromolecular flexibility. Generate Brownian Dynamics, Discrete Molecular Dynamics, and Normal Mode Analysis ensembles, then compare them with PCA.

FlexServBioExcel biobbPCA suiteDocker
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Molecular Structure Checking and Repair

Check and repair a raw PDB structure before Molecular Dynamics. Fix altlocs, disulfides, amides, and chirality, model missing atoms with Modeller, then minimize with AMBER sander.

BioExcel biobbModellerAMBERDocker
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Mutation Free Energy Calculations

Compute a mutation free energy with pmx and GROMACS by fast-growth non-equilibrium thermodynamic integration. Horus fans out the replicate TI transitions across executors.

pmxGROMACSBioExcel biobbDocker
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Protein Conformational Ensembles

Generate protein conformational ensembles with CONCOORD, FlexServ, NOLB and iMODS, then cluster and run PCA to get B-factors, hinge points, stiffness and collectivity.

CONCOORDFlexServNOLBiMODS
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Protein Conformational Transitions with GOdMD

Compute a conformational transition pathway between two protein states with GOdMD. The workflow fetches both structures, maps the residues with EMBOSS, and writes an XTC trajectory.

GOdMDBioExcel biobbEMBOSSAmberTools
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Protein-Ligand Docking (Cluster90 Binding Site)

Dock Imatinib into p38-alpha MAP kinase with AutoDock Vina. A PDB Cluster90 analysis of homologous structures locates the binding site and defines the docking box.

AutoDock VinaOpenBabelBioExcel biobbDocker
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Protein-Ligand Docking (PDBe REST API Binding Site)

Dock Dasatinib into p38-alpha MAP kinase with AutoDock Vina. The workflow queries the PDBe REST API for annotated binding sites instead of computing a cavity locally.

AutoDock VinaOpenBabelPDBe REST APIBioExcel biobb
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Protein-Ligand Docking with fpocket

Find the binding cavity on the receptor with fpocket, then dock the ligand with AutoDock Vina. Horus runs the biobb_vs stages in Docker and the rest in a native conda environment.

fpocketAutoDock VinaOpenBabelBioExcel biobb
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Protein-Membrane MD Analysis

Analyze a membrane MD simulation with biobb_mem, FATSLiM, and Lipyphilic. Compute bilayer thickness, order parameters, area per lipid, density, pore radius, and lipid flip-flop events.

BioExcel biobbFATSLiMLipyphilicMDAnalysis
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Engine capabilities

Small workflows that show one runtime capability each: fan-out, dynamic graphs, bounded loops, and subworkflows.

Bounded Loop with Range Map

A minimal Horus showcase of the bounded loop. The map construct takes a range instead of an upstream collection, so N clones run concurrently with no producer stage in front of them.

horus-runtimeYAMLuv
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Fan-out, Map and Gather

A minimal Horus showcase of the declarative map construct. A producer stage splits a collection into batches, the map block fans a stage out over every batch, and a gather stage collects the results.

horus-runtimeYAMLuv
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Programmatic Dynamic DAG

A Horus showcase of the runtime DAG-mutation API. A planning stage reads its data, then adds one processing stage per discovered group plus a fan-in stage, all from inside its own function.

horus-runtimePythonuv
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Subworkflow Reuse

A Horus showcase of the subworkflow construct. A sub block carries a complete child workflow, and a YAML anchor instantiates the same two-stage body twice under different prefixes.

horus-runtimeYAMLuv
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