Get the plugin!
The CavitOmiX PyMOL plugin is free, but you can contributed to our development fund. Every contribution helps us to improve the tool and will empower the scientific community.
How to install the plugin? Read more here:
A PyMol Plugin
Cavitomix is the art and science of making sense of the binding and interaction sites of biomolecules.
CavitOmiX plugin for PyMOL, a nifty tool that allows you to analyze protein cavities from any input structure. You can now dive deep into your proteins, Catalophore cavities and binding sites using crystal structures and state-of-the-art AI models from OpenFold (powered by NVIDIA’s BioNeMo service), DeepMind`s AlphaFold and ESMFold by Meta. Even more exciting: just enter any protein sequence and you will get the structure predicted by OpenFold or ESMFold loaded into your PyMOL within seconds
Functions
- Catalophore™ cavities can be calculated for molecules loaded in PyMOL
- Predict protein structures within seconds for any protein sequence using OpenFold by NVIDIA BioNeMo (coming soon!) and ESMFold by Meta
- DeepMind AlphaFold models can be retrieved via UniProt ID
- Analyze the hydrophobicity of your Catalophore™ cavities
- Protein structures can be retrieved from the PDB using the PDB code
- Mix and match all the above in a single entry, align the structures and get a quick overview
- Catalophore™ cavity calculation settings can be changed
- Each Catalophore™ cavity is an “residue” entry and each cavity point is an “atom”, so you can select, remove, copy, represet cavities to your liking!
If you find CavitOmiX useful for your work, please cite it by stating something like:
“Cavities were calculated using CavitOmiX (v. 1.0, 2022, Innophore GmbH). For the analysis of the hydrophobicity of the cavities the corresponding hydrophobicity module of the program VASCo [1] was used. Cavities were calculated using a modified LIGSITE algorithm [2].”
Data collection statement
By downloading and using the CavitOmiX PyMOL plugin, you agree to the following:
Structure requests. To process your requests, the following data is collected: IP address, approximate location down to the level of a major city, and time of access. Your input (PDB code, UniProt ID, sequence, etc.) is forwarded to and processed by third-party services (RCSB PDB, the AlphaFold Protein Structure Database, ESMFold by Meta and NVIDIA BioNeMo). We have no control over the privacy practices of these services, and their own terms apply.
Usage statistics. Newer versions of the plugin, including the one bundled with InnoMOL, count the cavity calculations you run, so that we can see how the plugin is used and plan its development. For each finished calculation the plugin records the time, the plugin version, the protein size as a coarse range, the number of cavities found, the run time and whether it was a re-run, together with a random installation ID that the plugin creates. The structure itself, its name, PDB codes and sequences are never recorded or sent. The records are kept on your computer and sent to our server whenever it can be reached. The server also stores the IP address the installation last connected from, and links the records to your licence key if you use one.
You can switch usage statistics off at any time: write {"share_usage": false} to the file settings.json in the folder .pymol/cavitomix in your home directory, or set the environment variable CAVITOMIX_NO_USAGE=1. To have the records of your installation deleted, contact us as described in our Data Protection Declaration and quote the installation ID from the file install_id in the same folder.
Your information will not be sold or shared beyond the services named above.