Difference between revisions of "CavitOmiX"
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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] | + | * 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] |
| − | * [AlphaFold2] models can be retrieved via UniProt ID | + | * [https://alphafold.ebi.ac.uk AlphaFold2] models can be retrieved via [https://www.uniprot.org/ UniProt ID] |
* Cavities can be calculated for molecules loaded in PyMOL | * Cavities can be calculated for molecules loaded in PyMOL | ||
* Analyze the hydrophobicity of your cavities | * Analyze the hydrophobicity of your 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 an quick overview | * Mix and match all the above in a single entry, align the structures and get an quick overview | ||
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| − | [[File:.png|500px|thumb|center|CavitOmiX PyMOL plugin | + | [[File:.png|500px|thumb|center|CavitOmiX PyMOL plugin in cooperation with NVIDIA BioNeMo ]] |
| − | ==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]] | ||
Revision as of 08:19, 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.
- Predict protein structures within seconds for any protein sequence using OpenFold by NVIDIA BioNeMo (coming soon!) and ESMFold by Meta
- AlphaFold2 models can be retrieved via UniProt ID
- Cavities can be calculated for molecules loaded in PyMOL
- Analyze the hydrophobicity of your 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 an quick overview
- Cavity calculation setting scan be changed
- Each Cavity is an "residue" entry, each cavity point is an "atom", so you can select, remove, copy, represet cavities to your liking!
Overview
File:.png
CavitOmiX PyMOL plugin in cooperation with NVIDIA BioNeMo