GitHub - temple-compute/pantheon: Production-ready scientific workflows for the Horus Runtime: molecular dynamics, virtual screening, docking, LLM training and more. HPC pipelines that actually run at scale. · GitHub

/" data-turbo-transient="true" />

Skip to content

Type / to search

Sign in<br>Sign upAppearance settings

You signed in with another tab or window. Reload to refresh your session.<br>You signed out in another tab or window. Reload to refresh your session.<br>You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

{{ message }}

Uh oh!

There was an error while loading. Please reload this page.

temple-compute

pantheon

Public

Notifications<br>You must be signed in to change notification settings

Fork

Star<br>11

main

BranchesTags

Go to file

CodeOpen more actions menu

Folders and files<br>NameNameLast commit message<br>Last commit date<br>Latest commit

History<br>77 Commits<br>77 Commits

.github

.github

docs

docs

workflows

workflows

.gitignore

.gitignore

CONTRIBUTING.md

CONTRIBUTING.md

LICENSE

LICENSE

README.md

README.md

View all files

Repository files navigation

Horus Workflow Repository

Production-ready scientific workflows for the Horus Runtime . Molecular dynamics, virtual screening, docking, LLM training, and more. Each workflow is a multi-stage pipeline that routes every stage to the right cluster type automatically: HPC, cloud, or local.

Why Pantheon? Stop writing glue code. Declare your pipeline once and Horus runs it across heterogeneous compute, streams logs live, retries failures, and produces typed artifacts you can trace.

Star the repo ⭐ if you build scientific pipelines, it helps more people find these workflows.

Each workflow directory contains:

README.md: purpose, pipeline, install steps, and configuration guide

workflow.yaml or run.py: a plain Horus workflow definition or Python workflow builder

scripts/: small stage scripts and helper code when needed

Getting Started

# 1. Install uv (recommended)<br>curl -LsSf https://astral.sh/uv/install.sh | sh

# 2. Clone this repo<br>git clone https://github.com/temple-compute/pantheon<br>cd pantheon

# 3. Install horus-runtime from inside any workflow directory<br>cd workflows/drug-discovery/w01-boltz2-virtual-screening<br>uv sync<br># or, if you prefer pip:<br># pip install horus-runtime horus-environments

# 4. Run the workflow<br>uv run horus run workflow.yaml

BioExcel workflows also require a conda-family tool (micromamba, mamba, or conda) on your PATH. Their executors build conda environments to provision GROMACS, AMBER, and related simulation tools. More on executors at docs.templecompute.com.

Workflows

Drug Discovery

ID<br>Workflow<br>Description

W-01<br>Boltz-2 Virtual Screening<br>Predict binding structure and affinity for a protein–ligand library using Boltz-2

W-02<br>AutoDock Vina Docking<br>End-to-end molecular docking with AutoDock Vina: prep → dock → rank

W-32<br>DrugFlow + Boltz-2 Affinity<br>Generate pocket-conditioned molecules with DrugFlow, then score each one for binding affinity (ΔG) with Boltz-2

BioExcel Building Blocks

ID<br>Workflow<br>Description

W-03<br>GROMACS MD Setup<br>Full MD setup for lysozyme 1AKI using GROMACS: topology → solvation → equilibration → production MD

W-04<br>Ligand Parameterization<br>Generate GROMACS force-field parameters for a small-molecule ligand via OpenBabel and ACPype/GAFF

W-05<br>AMBER MD Setup<br>Full MD setup for lysozyme 1AKI using AMBER: LEaP topology → solvation → equilibration → production MD + analysis

W-09<br>GROMACS Protein-Ligand Complex MD Setup<br>Full MD setup for a T4 lysozyme–ligand complex using GROMACS, AMBER99SB-ILDN, and GAFF/ACPype ligand parameters

W-10<br>Mutation Free Energy Calculations<br>Non-equilibrium alchemical mutation free-energy (ΔΔG) via GROMACS + pmx, estimated with CGI/BAR/Jarzynski

W-11<br>Protein-Ligand Docking (Cluster90)<br>AutoDock Vina virtual screening with the docking box inferred from a PDB Cluster90 homolog analysis

W-12<br>Protein-Ligand Docking (PDBe REST API)<br>AutoDock Vina virtual screening with the docking box located via the PDBe REST API's annotated binding sites

W-13<br>Protein-Ligand Docking (fpocket)<br>AutoDock Vina virtual screening with the docking box computed directly from fpocket cavity detection

W-14<br>AMBER Protein MD Setup<br>Full AMBER (AmberTools/sander/cpptraj) MD setup and analysis for lysozyme 1AKI

W-15<br>AMBER Protein-Ligand Complex MD Setup<br>AMBER MD setup for a T4 lysozyme–ligand complex with ACPype/GAFF ligand parameterization

W-16<br>AMBER Constant pH MD Setup<br>Constant-pH MD with AmberTools, predicting per-residue pKa values from titratable-residue protonation states

W-17<br>DNA Helical Parameters<br>Extracts per-base-pair helical parameters and dynamics from a DNA MD trajectory using Curves+/Canal

W-18<br>ABC MD Setup<br>Ascona B-DNA Consortium standard protocol for DNA MD system preparation with AmberTools

W-19<br>Protein Conformational Ensembles<br>Generates and compares protein conformational ensembles via CONCOORD, ANM, FlexServ, NOLB, and iMODS

W-20<br>Protein...