alphafold
Open source code for AlphaFold. (by google-deepmind)
RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold (by RosettaCommons)
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| alphafold | RoseTTAFold | |
|---|---|---|
| 35 | 10 | |
| 11,683 | 1,928 | |
| 2.4% | 4.4% | |
| 6.4 | 0.0 | |
| 4 days ago | 2 months 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.
alphafold
Posts with mentions or reviews of alphafold.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-07.
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What is a recent scientific discovery that you find exciting?
For all you programmer types, these are the repos for each of them. AlphaFold - ProGen - ProtGPT2
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RFdiffusion: Diffusion model generates protein backbones
2. https://github.com/deepmind/alphafold
- GitHub - deepmind/alphafold: Open source code for AlphaFold.
- New Code Update to AlphaFold 2.0 (links in comments)
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What happened in tech in 2022
b. But seriously, AlphaFold2 dramatically improved the ability to predict protein structures. If you want to read a lot more about it go here or check out the code at https://github.com/deepmind/alphafold
- New Update To AlphaFold 2 (links in comments)
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The anti-vaccine movement and pro-Russian propaganda in social media – a summary report. Since the beginning of the war in Ukraine, there has been a trend in which anti-vaccine accounts have been changing their narrative towards supporting Kremlin propaganda.
If you’re asking about the literal actual sequence of mRNA in the various vaccines, that’s available online, and you can check that it makes the correct shape using a tool like AlphaFold
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Stability AI backs effort to bring machine learning to biomed
Their code/weights/everything.
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Nvida tool kit?
looks like the container uses GPUs for compute https://github.com/deepmind/alphafold
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AlphaFold reveals the structure of the protein universe
> but other famous labs have already moved to ML predictions and are competitive with DeepMind now.
it seems obvious this was going to happen, because https://github.com/deepmind/alphafold
RoseTTAFold
Posts with mentions or reviews of RoseTTAFold.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-11-26.
-
Paired MSAs
so far the options are: - https://github.com/RosettaCommons/RoseTTAFold/tree/main/example/complex_modeling : look for make_joint_MSA_bacterial.py. For eukaryotes you're out of luck. - https://zhanggroup.org/cpxDeepMSA/ haven't tested it yet. waiting for results. - if you already have MSAs for individual proteins you can try to map some with taxidID (if they have it provided in the Uniref header). Still looking for some more elaborate methods using phylogeny.
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Scaffolding protein functional sites using deep learning [pdf]
Code for RoseTTAFold: Accurate prediction of protein structures and interactions using a 3-track network
https://github.com/RosettaCommons/RoseTTAFold
- Meta Unveils New AI Supercomputer
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roseTTA fold trimer prediction
In the science article, they use it to predict theoretical structures of heterotrimers (https://www.science.org/doi/10.1126/science.abj8754) , however upon looking in their github (https://github.com/RosettaCommons/RoseTTAFold) they only seem to have prodcedure for predicting complexes of heterodimers. I've successfully done the procedure to predict heterodimers of proteins of interest to our lab, but cannot figure out how to predict trimers from the github
- Deep-learning algorithms can now predict a protein’s 3D shape from its linear sequence — a huge boon to structural biologists
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Putting the power of AlphaFold into the world’s hands
Baker Lab (https://www.bakerlab.org/) is cutting edge in that area and also has a protein prediction open source package (https://github.com/RosettaCommons/RoseTTAFold)
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Structure prediction discussion (AlphaFold2, RoseTTAfold)
RoseTTAfold paper , GitHub
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AlphaFold 2 open-sourced by DeepMind
and RoseTTAFold is here: https://github.com/RosettaCommons/RoseTTAFold
- DeepMind's AlphaFold is now Open Source
- RoseTTAFold: Accurate prediction of protein structures and interactions
What are some alternatives?
When comparing alphafold and RoseTTAFold you can also consider the following projects:
tensorflow - An Open Source Machine Learning Framework for Everyone
ColabFold - Making Protein folding accessible to all!
gym - A toolkit for developing and comparing reinforcement learning algorithms.
Visual Studio Code - Visual Studio Code
RFdiffusion - Code for running RFdiffusion
online-go.com - Source code for the Online-Go.com web interface
bypass-paywalls-chrome - Bypass Paywalls web browser extension for Chrome and Firefox.
developer-roadmap - Interactive roadmaps, guides and other educational content to help developers grow in their careers.
TheAlgorithms - All Algorithms implemented in Python
awesome-for-beginners - A list of awesome beginners-friendly projects.
Vue.js - This is the repo for Vue 2. For Vue 3, go to https://github.com/vuejs/core
DeepFaceLab - DeepFaceLab is the leading software for creating deepfakes.
alphafold vs tensorflow
RoseTTAFold vs ColabFold
alphafold vs gym
alphafold vs Visual Studio Code
alphafold vs RFdiffusion
alphafold vs online-go.com
alphafold vs bypass-paywalls-chrome
alphafold vs developer-roadmap
alphafold vs TheAlgorithms
alphafold vs awesome-for-beginners
alphafold vs Vue.js
alphafold vs DeepFaceLab