comparison alphafold.xml @ 7:eb085b3dbaf8 draft

"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"

6:04e95886cf24

        This is especially useful in screening drug candidates.
    - Protein-protein interactions
        Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
        To predict these interactions, other programs may ingest 3D models predicted by AlphaFold. Proprietary softwares include `GOLD <https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/>`_ and `SeeSAR <https://www.biosolveit.de/SeeSAR>`_, but many `free and open-source options <https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software>`_ are available such as `AutoDock <https://autodock.scripps.edu/>`_ and `SwissDock <http://www.swissdock.ch/>`_.

    *Expected run times*

    .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold_runtime_graph.png?raw=true
        :height: 520
        :alt: Run time graph

    |
    | In general, we observe a quadratic relationship between sequence length and time to fold.
    | Once your job begins, a sequence of 50aa will take approximately 1hr to complete, while a sequence of 2000aa will take about 18hrs.
    |

    **Input**

    *Amino acid sequence*

    | AlphaFold accepts a **single amino acid sequence** in FASTA format.

7:eb085b3dbaf8

        This is especially useful in screening drug candidates.
    - Protein-protein interactions
        Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
        To predict these interactions, other programs may ingest 3D models predicted by AlphaFold. Proprietary softwares include `GOLD <https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/>`_ and `SeeSAR <https://www.biosolveit.de/SeeSAR>`_, but many `free and open-source options <https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software>`_ are available such as `AutoDock <https://autodock.scripps.edu/>`_ and `SwissDock <http://www.swissdock.ch/>`_.

    **Input**

    *Amino acid sequence*

    | AlphaFold accepts a **single amino acid sequence** in FASTA format.