openfold
tape
| openfold | tape | |
|---|---|---|
| 3 | 1 | |
| 2,392 | 620 | |
| 1.9% | 0.0% | |
| 9.4 | 0.0 | |
| 3 days ago | over 1 year ago | |
| Python | Python | |
| Apache License 2.0 | BSD 3-clause "New" or "Revised" License |
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
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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
tape
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ProteinBERT: A universal deep-learning model of protein sequence and function
We evaluated based on downstream tasks (multiple supervised benchmarks, including 4 from TAPE), not the LM performance.
What are some alternatives?
FastFold - Optimizing AlphaFold Training and Inference on GPU Clusters
protein-bert-pytorch - Implementation of ProteinBERT in Pytorch
af2complex - Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
fashion-mnist - A MNIST-like fashion product database. Benchmark :point_down:
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.
beir - A Heterogeneous Benchmark for Information Retrieval. Easy to use, evaluate your models across 15+ diverse IR datasets.
Senpwai - A desktop app for tracking and batch downloading anime
evodiff - Generation of protein sequences and evolutionary alignments via discrete diffusion models
ProFET - ProFET: Protein Feature Engineering Toolkit for Machine Learning
text - Models, data loaders and abstractions for language processing, powered by PyTorch
pypdb - A Python API for the RCSB Protein Data Bank (PDB)
protein_bert