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 Schrodinger’s 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 CovitOmiX PyMol plugin, you agree to the following:
To process your requests, the following data will be collected: IP address, inferred geographic location down to the level of a major city, time of access. In addition, your input data (pdb code, sequence, etc.) is collected and shared and processed by third party organizations (OpenFold by NVIDIA BioNeMo, ESMFold by Meta DeepMind, AlphaFold and RCSB PDB). We have no control over the privacy practices of third-party organizations or individuals and different practices apply here.
Your information will not be sold or otherwise shared.