CavitOmiX: Difference between revisions
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==CavitOmiX 1.0== | ==CavitOmiX 1.0== | ||
CavitOmiX plugin for Schrodinger’s | 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]. | [https://innophore.com/cavitomix CavitOmiX]. | ||
* Predict protein structures within seconds for any protein sequence using [OpenFold by NVIDIA BioNeMo] (coming soon!) and [ESMFold by Meta] | * 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 cavities | * Analyze the hydrophobicity of your Catalophore™ cavities | ||
* Protein structures can be retrieved from the [PDB] using the PDB code | * 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 | |||
* Mix and match all the above in a single entry, align the structures and get | * 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! | ||
* Each [https://innophore.com | |||
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[[File:.png| | [[File:cavitomix-plugin-V1.0_screenshot.png|600px|thumb|center|CavitOmiX PyMOL plugin with BioNeMo by NVIDIA]] | ||
==References== | ==References & Information== | ||
# [https://innophore.com Innophore GmbH] | # [https://innophore.com Innophore GmbH] | ||
# [NVIDIA BioNeMo] | # [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:Surfaces and Voids|CavitOmiX]] | ||
[[Category:Biochemical_Properties]] | [[Category:Biochemical_Properties]] | ||
[[Category:Modeling and Editing Structures]] | |||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:Pymol-script-repo]] | [[Category:Pymol-script-repo]] | ||
[[Category:NVIDIA]] | [[Category:NVIDIA]] | ||
[[Category:BioNeMo]] | [[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
