This project is archived and is no longer under active development.
Thank you to everyone who used or contributed to this project. If you're interested in maintaining a fork, please feel free to do so
nf-core/plumb is a pipeline that generates a publicly accessible database that integrates structural and thermodynamic data for diverse protein-ligand systems, prioritizing reproducibility. The database will be built from known protein-ligand complexes and include docked congeneric ligand series to represent a broad chemical space, with quality control processes to evaluate the quality of docked poses. This effort is conducted in conjunction with the Living Journal of Computational Molecular Sciences paper, “Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0],” which aims to create a fully self-consistent, open community resource and set of best practices free from any particular commercial vendor influence.
Blog Post #1: link
Blog Post #2: link
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.
Now, you can run the pipeline using:
nextflow run nf-core/plumb \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>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.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.