- recipe plinder
PLINDER: The Protein-Ligand INteraction Dataset and Evaluation Resource.
- Homepage:
- Documentation:
- Developer docs:
- License:
MIT AND Apache-2.0
- Recipe:
- Links:
Protein-ligand interactions are foundational to the understanding of science and discovery of therapies. However, to this date, no large, high quality datasets with real-life relevant evaluations exist.
PLINDER is an academic-industry collaboration to address this, driven by VantAI, NVIDIA, the Computational Structural Biology group at the University of Basel & SIB Swiss Institute of Bioinformatics - co-organizers of CASP, and MIT. We aim to provide a gold standard dataset and evaluations to push the field of computational protein-ligand interactions prediction forward.
- package plinder¶
- Versions:
0.2.26-0,0.2.25-3,0.2.25-2,0.2.25-1,0.2.25-0- Depends:
on biotite
>=1.0on cloudpathlib
on eval-type-backport
on foldseek
on gcsfs
on gemmi
on google-cloud-storage
on keyrings.google-artifactregistry-auth
on ligand-validation
on mmcif
on mmpdb
on mmseqs2
on mols2grid
on nbformat
on networkit
>=11.0on numpy
<2on omegaconf
on openbabel
on openstructure
on pandas
on plip
2.3.0on plotly
on posebusters
on pyarrow
on pydantic
on python
>=3.10on python-duckdb
on pytorch-cpu
on rdkit
>=2024.03.6on reduce
on six
on tabulate
on tqdm
on typing_extensions
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install plinder
to add into an existing workspace instead, run:
pixi add plinder
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install plinder
Alternatively, to install into a new environment, run:
conda create -n envname plinder
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/plinder:<tag>
(see plinder/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/plinder/README.html)
