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add new activity page and create software page
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‎_data/sidebars/main.yml‎

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url: /community_resources
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- title: How-to Guides
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url: /guides
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- title: Software
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url: /software
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- title: External resources
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subitems:
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- title: Structure prediction

‎_data/tool_and_resource_list.yml‎

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URL: protein_design_seminars
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DOI: https://doi.org/10.5281/zenodo.17626498
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- Description: A nextflow pipeline with support for numerous structure prediction tools.
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Tag: Community resource
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Tag: Software
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Title: nf-core ProteinFold v2.0.0
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Type:
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- Workflow
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Roadmap:
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- Roadmap deliverable 3
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URL: nfcore_proteinfold
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DOI: https://doi.org/10.5281/zenodo.7437037
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DOI: https://doi.org/10.5281/zenodo.7437037
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- Description: Predicts the structure of target proteins using MSAs generated by hhblits/jackhmmer.
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Tag: Software
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Title: AlphaFold2
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/611418237/Using+AlphaFold2+on+AMD+GPUs
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DOI:
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- Description: Predicts the structure of target molecules (proteins, nucleic acids, small molecules) using MSAs generated by MMSeqs2.
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Tag: Software
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Title: Boltz
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/1767571575/Using+Boltz+v.2.2.1+on+AMD+GPUs
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DOI:
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- Description: Predicts the structure of target proteins using MSAs generated by MMSeqs2.
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Tag: Software
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Title: ColabFold
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/611123341/Using+ColabFold+on+AMD+GPUs
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DOI:
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- Description: Predicts the structure of a target sequence using the ESM pre-trained language model.
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Tag: Software
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Title: ESMFold
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/1028816938/Using+ESMFold+on+AMD+GPUs
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DOI:
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- Description: Predicts a sequence composition compatible with an input target structure.
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Tag: Software
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Title: ProteinMPNN
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/613089393/Using+ProteinMPNN+on+AMD+GPUs
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DOI:
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- Description: Diffusion-based model to generate new protein structures.
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Tag: Software
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Title: RFdiffusion
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Type:
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- Software
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- For AMD GPUs
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Roadmap:
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- Roadmap deliverable 3
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URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/808091691/Using+RFDiffusion+on+AMD+GPUs
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DOI:

‎pages/activities/amd_software.md‎

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---
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title: Porting high priority software to AMD GPUs
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description: Porting software prioritised by the community to AMD to allow software execution at Pawsey Supercomputing Research Centre and other centres operating AMD GPUs.
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type: Activity_in_progress
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roadmap: A shared platform, or platforms (Roadmap D3Ab)
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roadmap_category: Shared-platform
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contributors: [Sarah Beecroft, Joshua Storm Caley]
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toc: false
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tiles:
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- title: "Visit the software resources page to see the tools ported to AMD GPUs"
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url: /software
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---
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{% include tiles-simple.html target = "tiles" col = "1" %}
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## Details
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- Deep Learning models work natively with NVIDIA hardware.
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- Setonix at Pawsey contains a large number of AMD GPUs.
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- Models can be made to work with AMD hardware available at Pawsey.
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- This ongoing activity is specifically for the identification, prioritisation, and porting of structural biology software from NVIDIA to AMD GPUs.
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### Completed
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- [AMD compatible containers for nf-core proteinfold](nfcore_proteinfold_pawsey).
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### In Progress
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### Future
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- Continue to port software to AMD that has been prioritised by the community.
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### Acknowledgements
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This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.

‎pages/activities/nfcore_proteinfold_pawsey.md‎

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---
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title: nf-core ProteinFold at Pawsey
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description: Deploy nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre.
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title: Porting software to AMD to enable nf-core ProteinFold at Pawsey
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description: Port software to AMD to allow the deployment of the nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre.
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type: Activity_in_progress
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roadmap: A shared platform, or platforms (Roadmap D3Ab)
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roadmap_category: Shared-platform
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contributors: [Sarah Beecroft, Joshua Storm Caley]
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toc: false
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redirect_from: /website/nfcore_proteinfold_pawsey
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tiles:
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- title: "Visit the software resources page to see the tools ported to AMD GPUs"
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url: /software
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- title: "See version 2.0.0 of the nf-core/proteinfold workflow"
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url: https://nf-co.re/proteinfold/2.0.0/
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---
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{% include tiles-simple.html target = "tiles" col = "2" %}
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## Details
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- Deep Learning models work natively with NVIDIA hardware.
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- Setonix at Pawsey contains a large number of AMD GPUs.
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- Models can be made to work with AMD hardware available at Pawsey.
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### Completed
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- Build AMD compatible container for AlphaFold2.
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- Adapt containers for compatibility with nf-core proteinfold.
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- Test nfcore proteinfold workflow at Pawsey.
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### In Progress
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- ProteinFold config optimized for Pawsey.
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### Future
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- Port software to AMD that has been prioritised by the community.
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### Acknowledgements
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This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.

‎pages/resources/software.md‎

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---
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title: Software
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page_id: software
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toc: false
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---
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The software listed here is the result of activities across the ASBC community. An additional label has been added to those activities that address a deliverable from the [infrastructure roadmap](https://doi.org/10.5281/zenodo.15786982).
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{% include resource-table-category.html category="Software" %}
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