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Structure Prediction

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Resource Description Type
AFDB Clusters Database Database of UniProt predicted structures clustered with foldseek
AFESM Clusters Database Database of UniProt and Metagenome predicted structures clustered with foldseek
Evolutionary Scale Modelling Atlas of structures 770 million ESMFold predicted structures -- much faster calculations as the don't relying on explicity co-evolutionary multiple sequence alignments
AlphaFold Protein Structure database 200 million AF2 predicted protein structures, with AlphaMissense etc included
Boltz Slack A slack channel to discuss developments of Boltz
ColabBio Discord A discord channel for asking questions related to the various Colab documents that are available
ELIXIR 3D-BioInfo European community for structural bioinformatics research
AlphaFold2, OpenFold, Protein Language Models and Beyond Detailed description of the machine learning concepts behind AI protein structure prediction methods
AlphaFold 5 minute explainer Overview of the AlphaFold pipeline by the New England Journal of Medicine
Boston Protein Design and Modeling Club ~1hr talks by method developers on recent breakthroughs in protein modelling
Running ColabFold notebook on a HPC Covers basics of ssh and jupyter notebooks on a HPC
Awesome Protein Structure Prediction and Design Software List A collection of software for protein structure prediction and design, with a focus on new deep learning and transformer based tools.
Biomolecular Structure Prediction Tools Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction.
AlphaFold3 explainer A visual walkthrough of the AlphaFold3 architecture
EMBL-EBI AlphaFold Guide EBI Guide to using AlphaFold and interpreting model outputs
AlphaFold3 Server Free Google service to run AlphaFold3. NON-COMMERICAL USE!
NeuroSnap Freemium service for deep learning structural biology software
Tamarind Bio Freemium service for deep learning structural biology software
ColabFold Notebooks Free structure prediction notebooks available to run on Google Colab platform
Australian AlphaFold Service Free AlphaFold2 service supported by the Australian Biocommons