af2complex
openfold
| af2complex | openfold | |
|---|---|---|
| 1 | 5 | |
| 125 | 2,407 | |
| - | 1.9% | |
| 1.8 | 9.4 | |
| about 1 year ago | 1 day ago | |
| Python | Python | |
| - | Apache License 2.0 |
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af2complex
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Is there any software that can predict if two amino acid sequences would interact?
Also, I saw a "AF2Complex" add-on to AlphaFold 2 which seems to do exactly what I'm looking for, but I don't think that it's available on ColabFold yet and I don't have TB storage available. I'm not expecting you to know this, but is there any way to run an AF2 add-on on Colab?
openfold
- AlphaFold 3 predicts the structure and interactions of all of life's molecules
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TIL : about the game "Foldit", a puzzle game about protein folding. In 2011, its gamers helped decipher a protein of a HIV-like virus, solving a scientific problem that went unsolved for 15 years in as little as 10 days.
Seeing this stuff on GitHub is mind-blowing: https://github.com/aqlaboratory/openfold
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[P] Detailed Explanation of how AlphaFold Works, Protein Folding and Design
I plan on writing another article about ESMFold and OmegaFold if you find this helpful! Let me know what you think, and DM me should you find any inaccuracies! Finally, a shoutout to OpenFold for their open-source AF2 code that allowed me to triple-check dimensionalities :)
- OpenFold: An open-source replication of Alphafold2
What are some alternatives?
ColabFold - Making Protein folding accessible to all!
FastFold - Optimizing AlphaFold Training and Inference on GPU Clusters
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
ProteinStructurePrediction - Protein structure prediction is the task of predicting the 3-dimensional structure (shape) of a protein given its amino acid sequence and any available supporting information. In this section, we will Install and inspect sidechainnet, a dataset with tools for predicting and inspecting protein structures, complete two simplified implementations of Attention based Networks for predicting protein angles from amino acid sequences, and visualize our predictions along the way.
Invariant-Attention - An implementation of Invariant Point Attention from Alphafold 2
tape - Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
awesome-protein-design - A curated list of awesome protein design research, software and resources.
Senpwai - A desktop app for tracking and batch downloading anime
Biopython - Official git repository for Biopython (originally converted from CVS)