About
Welcome! This website is the virtual meeting place for all users of computing for structural biology research in Australia. This page currently serves as a knowledge resource for use of Deep Learning methods in Structural Biology, but could expand to link together Cryo-EM processing and crystallographic methods in time. This page contains How-to Guides for the use of Deep Learning methods in Structural Biology as well as news items and announcements for relevant courses, meetings and information about structural biology. It can be what we make it!
Join the conversation
If you would like to, there are multiple ways to join the conversation. The most straightforward is to attend the next quarterly community meeting. If you join the mailing list (see below), you will receive community updates and automatic community meeting invitations.
You can also join the conversation by:
- Contributing to the discussion forum,
- Attending one of the upcoming community events
Current activities
A collaborative activity bringing together members of the computational structural biology community, infrastructure providers, and the Australian BioCommons, in order to determine how to increase access to RFdiffusion for life science researchers.
The Roadmap is in the final stages of drafting and will be announced here and directly to the community by the end of October.
Upcoming events
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BioMolecular Horizons
Launch of the website at BioMolecular Horizons 2024
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Computational Structural Biology Community Meeting
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Online
Visit the rolling agenda for details on how to join the next meeting.
News
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Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)
MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif)
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Script for Alphafold output validation metrics!
Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs)
Guides
Have you recently started using AlphaFold and want to include its structural predictions in your paper, but don't know the best way to do so? In this short guide, we clarify what you should include so That your work is clear and reproducible for the reader.
External resources
| How-to Guide or resource | Description | Category |
|---|---|---|
| Galaxy Australia | Free access to a high-performance computing network through a simple web interface for Australian Researchers | Webservers and computing resources |
| Australian AlphaFold Service | Access a full version of AlphaFold2 supported by the Australian Biocommons | Webservers and computing resources |
| Mastodon | Social media posting platform | Online communities |
| Bluesky | Social media posting platform | Online communities |
| ColabBio Discord | A discord channel for asking questions related to the various Colab documents that are available | Online communities |
| European Centre of Excellence for Computational Biomolecular Research | Talks focused on molecular dynamics simulations and computational chemistry | YouTube talks and tutorials |
| ChimeraX tutorials | Playlist of tutorials on how to use ChimeraX with command lines | YouTube talks and tutorials |
| Luminous Lab Blender tutorials | Blender tutorials for protein animations | YouTube talks and tutorials |
| Brady Johnston Blender tutorials | Blender tutorials for protein animations | YouTube talks and tutorials |
| 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 | YouTube talks and tutorials |
| AlphaFold 5 minute explainer - Medical Journal | Overview of the AlphaFold pipeline by the New England Journal of Medicine | YouTube talks and tutorials |
| Structural Biology Grid Consortium Talk Series | Talks focused on CryoEM but also computational structural biology and protein design | YouTube talks and tutorials |
| NeuroSnap protein design videos | 100 second videos on how to use various protein tools. Guides are with their clean proprietary interface | YouTube talks and tutorials |
| Boston Protein Design and Modeling Club | ~1hr talks by method developers on recent breakthroughs in protein modelling | YouTube talks and tutorials |
| ChimeraX outline selected area | ChimeraX how-to | Protein viz guides and tutorials |
| ChimeraX cavity visualisation | ChimeraX how-to | Protein viz guides and tutorials |
| ChimeraX recipes | Protein visualisation guides for UCSF ChimeraX | Protein viz guides and tutorials |
| Running ColabFold notebook on a HPC | Covers basics of ssh and jupyter notebooks on a HPC | Computational structural bio guides and tutorials |
| ColabFold tutorial | Three short tutorials for running ColabFold | Computational structural bio guides and tutorials |
| BLAST tutorial | Short how-to guide on using BLAST from the command line | Computational structural bio guides and tutorials |
| Amber tutorial | Molecular Dynamics simulation tutorials | Computational structural bio guides and tutorials |
| LAMMPS tutorials | Molecular Dynamics simulation tutorials | Computational structural bio guides and tutorials |
| GROMACS tutorials | Molecular Dynamics simulation tutorials | Computational structural bio guides and tutorials |
| GROMACS tutorials | Molecular Dynamics simulation tutorials | Computational structural bio guides and tutorials |
| ColabDesign notebooks | Google Colab notebooks for running protein design | Computational structural bio guides and tutorials |
| Pyrosetta tutorials | Collection of how-to guides for protein design | Computational structural bio guides and tutorials |
| Rosetta tutorial | User guide on protein design with Rosetta | Computational structural bio guides and tutorials |
| RFDiffusion | Walkthrough guide on running RFDiffusion | Computational structural bio guides and tutorials |
| HMMER tutorial | User guide for running HMMER on the command line | Computational structural bio guides and tutorials |
| HH-suite tutorial | User guide for running Hiden Markov Models of protein sequences on the command line | Computational structural bio guides and tutorials |
| MMseqs2 tutorial | User guide for running MMseqs from the command line | Computational structural bio guides and tutorials |
| Biomolecular Structure Prediction Tools | Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction. | Computational structural bio guides and tutorials |
| AlphaFold3 explainer | A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for. | Computational structural bio guides and tutorials |
| 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 | Computational structural bio guides and tutorials |
| NVIDIA Biology | NVIDIA web server and API for running protein design and structure prediction software (e.g. RFDiffusion, ESMFold, etc.) | Webservers and computing resources |
| BioTools | Curated search list of computational biology tools around the world | Webservers and computing resources |
| Pawsey Supercomputing Centre | Peak academic Australian Research Computing Facility | Webservers and computing resources |
| National Computing Infrastructure | Peak academic Australian Research Computing Facility | Webservers and computing resources |
| AlphaFold3 Server | AlphaFold3 provided by Google's webserver to their compute infrastructure. NON-COMMERICAL USE! | Webservers and computing resources |
| FoldSeek web server | Multiple Structure Alignment in a browser | Webservers and computing resources |
| 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 | Webservers and computing resources |
| AlphaFold Protein Structure database | 200 million AF2 predicted protein structures, with AlphaMissense etc included | Webservers and computing resources |
Contributors
The projects included here represent a joint effort by the following people at multiple Australian institutions.
James Lingford
Research Officer, Greening Lab, Monash University
Johan Gustafsson
Engagement, Australian BioCommons, University of Melbourne
Kate Michie
Chief Scientist, Structural Biology Facility UNSW
Keiran Rowell
Computational Scientist, Structural Biology Facility UNSW
Michael Healy
Postdoctoral Research Fellow, University of Queensland
