.. matcher documentation master file, created by sphinx-quickstart on Thu Aug 22 13:20:10 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. .. |AUR| image:: https://img.shields.io/aur/version/python-pyjess?logo=archlinux&style=flat&maxAge=3600 .. :target: https://aur.archlinux.org/packages/python-pyjess .. :class: dark-light EnzyMM - The Enzyme Motif Miner |Stars| ======================================= .. |Stars| image:: https://img.shields.io/github/stars/rayhackett/enzymm.svg?style=social&label=Star&maxAge=3600 :target: https://github.com/rayhackett/enzymm/stargazers :class: dark-light *Identify catalytic sites in protein structures with the Enzyme Motif Miner!* |Actions| |Coverage| |PyPI| |Wheel| |Docker| |Apptainer| |Versions| |versions| |License| |Source| |Issues| |Docs| |Changelog| |Downloads| |Preprint| .. |Actions| image:: https://img.shields.io/github/actions/workflow/status/RayHackett/enzymm/test.yml?branch=main&style=flat&maxAge=300 :target: https://github.com/RayHackett/Enzymm/actions/workflows/test.yml :class: dark-light .. |Coverage| image:: https://img.shields.io/codecov/c/gh/rayhackett/enzymm?logo=codecov&style=flat&maxAge=3600 :target: https://codecov.io/gh/rayhackett/enzymm/ :class: dark-light .. |PyPI| image:: https://img.shields.io/pypi/v/enzymm.svg?style=flat&maxAge=3600 :target: https://pypi.python.org/pypi/enzymm :class: dark-light .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/enzymm?style=flat&maxAge=3600 :target: https://anaconda.org/bioconda/enzymm :class: dark-light .. |Wheel| image:: https://img.shields.io/pypi/wheel/enzymm?style=flat&maxAge=3600 :target: https://pypi.org/project/enzymm/#files :class: dark-light .. |Docker| image:: https://img.shields.io/badge/Docker-GHCR-blue?logo=docker :target: https://github.com/users/rayhackett/packages/container/package/enzymm :class: dark-light .. |Apptainer| image:: https://img.shields.io/badge/Apptainer-SIF-blue?logo=apptainer&style=flat :target: https://github.com/rayhackett/enzymm/releases/latest :class: dark-light .. |Versions| image:: https://img.shields.io/pypi/pyversions/enzymm.svg?style=flat&maxAge=3600 :target: https://pypi.org/project/enzymm/#files :class: dark-light .. |versions| image:: https://img.shields.io/github/v/tag/rayhackett/enzymm?label=version&sort=semver :target: https://github.com/rayhackett/enzymm/tags :class: dark-light .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat&maxAge=3600 :target: https://choosealicense.com/licenses/mit/ :class: dark-light .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=3600&style=flat :target: https://github.com/rayhackett/enzymm/ :class: dark-light .. |Issues| image:: https://img.shields.io/github/issues/rayhackett/enzymm.svg?style=flat&maxAge=600 :target: https://github.com/rayhackett/enzymm/issues :class: dark-light .. |Docs| image:: https://img.shields.io/readthedocs/enzymm?style=flat&maxAge=3600 :target: http://enzymm.readthedocs.io/en/stable/?badge=stable :class: dark-light .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-green.svg?maxAge=3600&style=flat :target: https://github.com/rayhackett/enzymm/blob/main/CHANGELOG.md :class: dark-light .. |Downloads| image:: https://static.pepy.tech/personalized-badge/enzymm?period=total&units=INTERNATIONAL_SYSTEM&left_color=grey&right_color=GREEN&left_text=downloads :target: https://pepy.tech/projects/enzymm :class: dark-light .. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-firebrick?style=flat&maxAge=3600 :target: https://doi.org/10.64898/2026.02.10.705182 :class: dark-light Overview -------- **EnzyMM** is a Python tool to identify known patterns of catalytic residues in protein structures. We also provide a webserver where you can run **EnzyMM** on single queries `here `_. Catalytic sites, which define the function of proteins, are among the most conserved parts of enzyme structures. It makes sense therefore, that their similarities can be identified even if the rest of the protein has diverged throughout the course of evolutionary history. Similarly doing so immediately gives biological insight into possible functions. Proteins carry out a myriad of different functions. Yet constrained by the chemistry of life, given access to a toolkit of just 20 amino acids, often the same catalytic patters emerge. This means that by focusing on catalytic sites, functional convergence around similar mechanisms and structures can be detected. This makes **EnzyMM** fundamentally knowledge based and interpretable. While proteins are commonly explored and compared using sequence based methods, these suffer various drawbacks. Principally it is not immediately apparent which part of the sequence is most important. Secondly, sequence diverges much faster than structure obscuring similarities as proteins mutate and evolve. Sequence rearrangements can completely break certain approaches. With **PyJess** and **EnzyMM** we develop an extremely fast yet precise way to identify known catalytic patters without any of the drawbacks of sequence based methods. Thanks to very detail-oriented yet large scale curation efforts in the M-CSA and some `clever engineering `_ we can scan most protein structures against nearly 7000 catalytic arrangements in tenths of a second. Perfectly suited for exploring the expanding universe of predicted protein structures, we are excited to present **EnzyMM**! For further information please refer to our scientific preprint of EnzyMM titled `"Investigating Enzyme Function by Geometric Matching of Catalytic Motifs" `_ 🔧 Setup -------- **EnzyMM** is available for all modern Python versions (3.8+). Run ``pip install enzymm`` in a shell to download the latest release from PyPI, or have a look at the :doc:`Installation page ` to find other ways to install **EnzyMM**. Alternatively, we provide both Docker and Apptainer Images 🖼️. 📚 Library ---------- .. toctree:: :maxdepth: 2 :caption: Contents: User Guide API Reference 🔎 Related Projects ------------------- **EnzyMM** draws on a library of catalytic templates derived by Ioannis Riziotis from the `Mechanism and Catalytic Site Atlas `_ which is developed at the `Thornton Group `_ and maintained by Antonio Ribeiro. **EnzyMM** utilizes **PyJess**, a `Cython `_ wrapper of `JESS `_, for finding matches between templates and query structures. **PyJess** was developed by Martin Larralde. Please have a look at `PyJess `_! 🔖 Citations ------------ **EnzyMM** is academic software but relies on many previous approaches. We kindly ask you to cite both: - **EnzyMM**, for instance as: - Hackett RE et al. (2026), Investigating Enzyme Function by Geometric Matching of Catalytic Motifs [Preprint], BioRxiv, `DOI:10.64898/2026.02.10.705182 `_ - **Mechanism and Catalytic Site Atlas** as: - Ribeiro AJM et al. (2017), Nucleic Acids Res, 46, D618-D623. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. `DOI:10.1093/nar/gkx1012. PMID:29106569 `_. ⚖️ License ---------- **EnzyMM** is provided under the `MIT License `_. Both **PyJess** and the original **JESS** code are distributed under the `MIT License `_ as well. Though conceived at the `EMBL-EBI `_ in Hinxton, UK in the `Thornton Group `_, **EnzyMM** is now developed by Raymund Hackett and the `Zeller Group `_ at the `Leiden University Medical Center `_ in Leiden in the Netherlands with continuing support from the Thornton Group.