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|type = plugin | |type = plugin | ||
|download = https://innophore.com/cavitomix | |download = https://innophore.com/cavitomix | ||
|author = Innophore Team | |author = [https://www.linkedin.com/in/georg-steinkellner-81b2bbb9 Georg Steinkellner], [https://www.linkedin.com/in/christiancgruber Christian C. Gruber], [https://www.linkedin.com/in/karl-gruber-2a486135 Karl Gruber]*, and the [https://www.linkedin.com/company/innophore Innophore Team] | ||
|homepage = https://innophore.com | |homepage = https://innophore.com | ||
}} | }} | ||
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[[File:Cavitomix.png|400px|center]] | [[File:Cavitomix.png|400px|center]] | ||
==CavitOmiX 1.0== | |||
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, 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. | |||
[https://innophore.com/cavitomix CavitOmiX]. | |||
* Catalophore™ Cavities can be calculated for molecules loaded in PyMOL | |||
* Predict protein structures within seconds for any protein sequence using [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold] by NVIDIA [https://www.nvidia.com/en-us/gpu-cloud/bionemo BioNeMo] (coming soon!) and [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold by Meta] | |||
* [https://www.deepmind.com/research/highlighted-research/alphafold AlphaFold] models can be retrieved via [https://www.uniprot.org/ UniProt ID] | |||
* Analyze the hydrophobicity of your Catalophore™ cavities | |||
* Protein structures can be retrieved from the [https://www.rcsb.org/ 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 [https://innophore.com Catalophore™ cavity] is an "residue" entry and each cavity point is an "atom", so you can select, remove, copy, represent cavities to your liking! | |||
==Overview== | |||
* | |||
* | |||
[[File:cavitomix-plugin-V1.0_screenshot.png|600px|thumb|center|CavitOmiX PyMOL plugin with BioNeMo by NVIDIA]] | |||
==References & Information== | |||
# [https://innophore.com Innophore GmbH] | |||
# [https://www.nvidia.com/en-us/gpu-cloud/bionemo NVIDIA BioNeMo] | |||
# [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold by Meta] | |||
# [https://alphafold.ebi.ac.uk AlphaFold2] | |||
[[Category:Surfaces and Voids|CavitOmiX]] | |||
[[Category:Biochemical_Properties]] | |||
[[Category:Modeling and Editing Structures]] | |||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:Pymol-script-repo]] | [[Category:Pymol-script-repo]] | ||
[[Category:NVIDIA]] | |||
[[Category:BioNeMo]] | |||
Latest revision as of 21:24, 23 December 2022
| Type | PyMOL Plugin |
|---|---|
| Download | https://innophore.com/cavitomix |
| Author(s) | Georg Steinkellner, Christian C. Gruber, Karl Gruber*, and the Innophore Team |
| License | |
| https://innophore.com | |
CavitOmiX 1.0
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, 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.
- 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
- 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, represent cavities to your liking!
Overview
