- 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:
0.2.25-2,0.2.25-1,0.2.25-0- depends biotite:
>=1.0- depends cloudpathlib:
- depends eval-type-backport:
- depends foldseek:
- depends gcsfs:
- depends gemmi:
- depends google-cloud-storage:
- depends keyrings.google-artifactregistry-auth:
- depends ligand-validation:
- depends mmcif:
- depends mmpdb:
- depends mmseqs2:
- depends mols2grid:
- depends nbformat:
- depends networkit:
>=11.0- depends numpy:
<2- depends omegaconf:
- depends openbabel:
- depends openstructure:
- depends pandas:
- depends plip:
2.3.0- depends plotly:
- depends posebusters:
- depends pyarrow:
- depends pydantic:
- depends python:
>=3.10- depends python-duckdb:
- depends pytorch-cpu:
- depends rdkit:
>=2024.03.6- depends reduce:
- depends six:
- depends tabulate:
- depends tqdm:
- depends typing_extensions:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install plinder and update with:: mamba update plinder
To create a new environment, run:
mamba create --name myenvname plinder
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/plinder:<tag> (see `plinder/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/plinder/README.html)
