The structural biology collection is maintained by the Australian Structural Biology Community. The collection and the community focuses on resources that help you learn about computational and deep Learning methods in Structural Biology.
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Skip resource table| Resource | Description | Topic(s) | Format | Provider |
|---|---|---|---|---|
| AlphaFold2, OpenFold, Protein Language Models and Beyond | Nazim Bouatta | Detailed and lucid talk on understanding the machine learning concepts behind AI protein structure prediction methods
|
Short Video | Community member | |
| AlphaFold 5 minute explainer - Medical Journal | Overview of the AlphaFold pipeline by the New England Journal of Medicine
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Short Video | NEJM | |
| AlphaFold2 How-to Guide | Step-by-step guide to help you to understand how the AlphaFold2 algorithm works and how to interpret the output data.
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Structure prediction | Guide | Australian Structural Biology Community |
| AlphaFold3 explainer | A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for.
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Structure prediction | Guide | Community member |
| Amber tutorial | Molecular Dynamics simulation tutorials
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Molecular dynamics | Guide | Community member |
| Best practices for presenting and sharing AlphaFold models in a paper | A guide to help new-comers get up to speed on presenting and sharing AlphaFold models in papers.
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Structure prediction | Guide | Australian Structural Biology Community |
| Biomolecular Structure Prediction Tools | Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction.
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Structure prediction | Guide | Community member |
| BLAST tutorial | Short how-to guide on using BLAST from the command line
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Guide | tinybio | |
| Boston Protein Design and Modeling Club | ~1hr talks by method developers on recent breakthroughs in protein modelling
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Webinar | Community member | |
| Brady Johnston Blender tutorials | Blender tutorials for protein animations
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Short Video | Community member | |
| ChimeraX cavity visualisation | ChimeraX how-to
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Guide | Community member | |
| ChimeraX outline selected area | ChimeraX how-to
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Guide | Community member | |
| ChimeraX recipes | Protein visualisation guides for UCSF ChimeraX
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Protein visualisation | Guide | Community member |
| ChimeraX tutorials | Playlist of tutorials on how to use ChimeraX with command lines
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Short Video | Community member | |
| ColabDesign notebooks | Google Colab notebooks for running protein design
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Guide | Community member | |
| ColabFold tutorial | Three short tutorials for running ColabFold
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Structure prediction | Guide | Community member |
| EMBL-EBI AlphaFold Guide | The best way to get up to competency with using an interpreting AlphaFold. Should be done by all grad students using AF
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Structure prediction | Online tutorial | EMBL-EBI |
| European Centre of Excellence for Computational Biomolecular Research | Talks focused on molecular dynamics simulations and computational chemistry
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Short Video | Community member | |
| GROMACS tutorials | Molecular Dynamics simulation tutorials
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Molecular dynamics | Guide | Community member |
| GROMACS tutorials | Molecular Dynamics simulation tutorials
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Molecular dynamics | Guide | Community member |
| HH-suite tutorial | User guide for running Hiden Markov Models of protein sequences on the command line
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Guide | Community member | |
| HMMER tutorial | User guide for running HMMER on the command line
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Guide | Community member | |
| LAMMPS tutorials | Molecular Dynamics simulation tutorials
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Molecular dynamics | Guide | Community member |
| Luminous Lab Blender tutorials | Blender tutorials for protein animations
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Short Video | Community member | |
| MMseqs2 tutorial | User guide for running MMseqs from the command line
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Guide | Community member | |
| NeuroSnap protein design videos | 100 second videos on how to use various protein tools. Guides are with their clean proprietary interface
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Short Video | Community member | |
| Pyrosetta tutorials | Collection of how-to guides for protein design
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Guide | Community member | |
| RFDiffusion | Walkthrough guide on running RFDiffusion
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Guide | Community member | |
| Rosetta tutorial | User guide on protein design with Rosetta
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Guide | Community member | |
| Running ColabFold notebook on a HPC | Covers basics of ssh and jupyter notebooks on a HPC
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Guide | Community member | |
| Structural Biology Grid Consortium Talk Series | Talks focused on CryoEM but also computational structural biology and protein design
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Short Video | Community member |