Iktos Engine

This repository contains a reference client implementation for our Iktos Engine: a set of focused, production-scale APIs for 3D virtual screening workflows spanning both ligand-based and structure-based regimes.

For more technical depth, see the Iktos 3D Engine technical report in this repository.

APIs

• Iktos 3D Align

  • Accurate ligand alignment method, useful for 3D ligand-based (LB) virtual screening.

• Iktos 3D Dock

  • Accurate template-based docking method, useful for 3D structure-based (SB) virtual screening.

• Boltz 3D Affinity

  • Reuses the Boltz-2 affinity trunk (Passaro et al., 2025) to score binding affinity directly from a user-supplied protein–ligand complex, without the time-consuming cofolding step.

Repository layout

• 3d-align/: notebooks, client code, and benchmark assets for the Iktos 3D Align API integration.
• 3d-dock/: notebooks, client code, and benchmark assets for the Iktos 3D Dock API integration.
• boltz-3d-affinity/: notebooks, client code, and benchmark assets for the Boltz 3D Affinity API integration.
• virtual-screening-pipeline/: virtual screening pipelines combining these APIs — virtual_screening_pipeline_A.ipynb (full 3D Align → 3D Dock → Boltz 3D Affinity) and virtual_screening_pipeline_B.ipynb (3D Dock → Boltz 3D Affinity, skips Align). See virtual-screening-pipeline/README.md for how to run them, and example data under virtual-screening-pipeline/data/.
• Iktos_3D_Engine_Technical_Report.pdf : technical report with additional implementation and performance details on Iktos Engine and the APIs above. Open this PDF for deeper context beyond the README and example notebooks.

Getting started

Set up an isolated environment using any tool of your choice (venv, conda, uv, …), then install dependencies from the repo root:

# example with venv
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Access & Contact

To request access or learn more, reach out at contact@iktos.com.

Status

This is an initial release of the Engine APIs and supporting materials; the repository will evolve as additional endpoints, examples, and benchmarking utilities are added.

Disclaimer

This source code project is provided as an example for educational and illustrative purposes only. While efforts have been made to ensure the accuracy and reliability of the code, no guarantee is made regarding its suitability for any specific purpose.

By accessing and using this source code, you agree that:

1. The code is provided "as is" without warranty of any kind, express or implied.
2. You acknowledge that you are solely responsible for any consequences resulting from the use of this code.
3. The author(s) and contributors of this code shall not be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) arising in any way out of the use of this code, even if advised of the possibility of such damage.
4. Copyright © 2026 Iktos. All rights reserved.

This disclaimer does not limit or exclude any liability for death or personal injury resulting from negligence, fraud, or any other liability that cannot be excluded or limited under applicable law.

Use of this source code project implies acceptance of these terms.