Research Object Crate for Bindflow

# Australian-Structural-Biology-Computing/bindflow [](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/ci.yml) [](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.XXXXXXX) [](https://www.nf-test.com) [](https://www.nextflow.io/) [](https://docs.conda.io/en/latest/) [](https://www.docker.com/) [](https://sylabs.io/docs/) [](https://cloud.seqera.io/launch?pipeline=https://github.com/Australian-Structural-Biology-Computing/bindflow) ## Introduction **Australian-Structural-Biology-Computing/bindflow** is a bioinformatics pipeline that generates protein binders for user-defined hotspot residues on a target protein structure. The pipeline will be executed until a user-defined number of designs pass the in-silico quality control criteria.  Bindflow is a wrapper around the BindCraft tool to allow convenient execution on HPC infrastructure. BindCraft includes 4 core binder design modules within a single tool. 1. Structure proposal (AlphaFold2 multimer hallucination) 2. Sequence design (SolubleMPNN) 3. Structure prediction (AlphaFold2) 4. Post-design quality control (PyRosetta) > [!WARNING] Post-design QC filtering is conducted with PyRosetta. Users must agree to the PyRosetta license terms. ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv id,binder_name,starting_pdb,chains,target_hotspot_residues,min_length,max_length,number_of_final_designs,settings_advanced,settings_filters demo,PDL1,PDL1.pdb,A,"56",65,150,10,default_4stage_multimer.json,default_filters.json ``` Each row represents a single design instance. Detailed documentation describing job parameters can be found in the BindCraft [documentation](https://github.com/martinpacesa/BindCraft). Briefly: - **id** is a unique job identifier - **binder_name** is an identifier for the protein target. - **starting_pdb** contains the target structure in PDB format. - **chains** defines the target chains in the starting_pdb. - **target_hotspot_residues** defines the residue indices of the target_pdb which will be targeted by the design process. - **min_length** defines the minimum length of the designed binder. - **max_length** defines the maximum length of the designed binder. - **number_of_final_designs** defines the number of binders required to pass QC criteria before the job is complete. - **settings_advanced** defines advanced BindCraft settings (JSON format). - **settings_filters** defines advanced BindCraft filter settings (JSON format). Workloads can be distributed over multiple GPUs by setting the --batches command line argument to split the number of final designs in to separate batches. Now, you can run the pipeline using: ```bash nextflow run Australian-Structural-Biology-Computing/bindflow \ -profile \ --input samplesheet.csv \ --outdir --batches 1 ``` > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). ## Credits Australian-Structural-Biology-Computing/bindflow was originally written by Ziad Al-Bkhetan. We thank the following people for their extensive assistance in the development of this pipeline: ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). ## Citations An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

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