openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2 (by aqlaboratory)
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. (by victor369basu)
| openfold | ProteinStructurePrediction | |
|---|---|---|
| 3 | 1 | |
| 2,392 | 10 | |
| 1.9% | - | |
| 9.4 | 0.0 | |
| 2 days ago | over 1 year ago | |
| Python | Python | |
| Apache License 2.0 | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
openfold
Posts with mentions or reviews of openfold.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-22.
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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
ProteinStructurePrediction
Posts with mentions or reviews of ProteinStructurePrediction.
We have used some of these posts to build our list of alternatives
and similar projects.
-
[P]Attention Based Protein Structure Prediction
If you like my work please consider staring the GitHub repo - https://github.com/victor369basu/ProteinStructurePrediction
What are some alternatives?
When comparing openfold and ProteinStructurePrediction you can also consider the following projects:
FastFold - Optimizing AlphaFold Training and Inference on GPU Clusters
Avolition2 - 3D action-RPG game for Linux/Windows/MacOS written in Python3 based on Panda3D engine
af2complex - Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
progen - Official release of the ProGen models
tape - Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
NoLabs - Open source biolab
Senpwai - A desktop app for tracking and batch downloading anime