FastFold
openfold
| FastFold | openfold | |
|---|---|---|
| 2 | 3 | |
| 506 | 2,392 | |
| - | 1.3% | |
| 0.0 | 9.4 | |
| 10 months ago | about 8 hours ago | |
| Python | Python | |
| Apache License 2.0 | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
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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.
FastFold
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👉 Impressed With AlphaFold? Checkout This Protein Structure Prediction Model (FastFold) That Reduces AlphaFold’s Training Time From 11 Days To 67 Hours
Code for https://arxiv.org/abs/2203.00854 found: https://github.com/hpcaitech/FastFold
Github: https://github.com/hpcaitech/FastFold
openfold
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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?
torchsynth - A GPU-optional modular synthesizer in pytorch, 16200x faster than realtime, for audio ML researchers.
af2complex - Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
warp-drive - Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning Framework on a GPU (JMLR 2022)
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.
torchrec - Pytorch domain library for recommendation systems
tape - Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
TransformerEngine - A library for accelerating Transformer models on NVIDIA GPUs, including using 8-bit floating point (FP8) precision on Hopper and Ada GPUs, to provide better performance with lower memory utilization in both training and inference.
Senpwai - A desktop app for tracking and batch downloading anime
autocvd - Tool to automatically set CUDA_VISIBLE_DEVICES based on GPU utilization. Usable from command line and code.