recipe alphafill

Transplant missing compounds to the AlphaFold models

Homepage:

https://alphafill.eu

Documentation:

https://alphafill.eu/manual

Developer docs:

https://github.com/PDB-REDO/alphafill

License:

BSD / BSD-2-Clause

Recipe:

/alphafill/meta.yaml

Links:

doi: 10.1038/s41592-022-01685-y

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing ligands, cofactors and (metal) ions to the AlphaFold models. By adding the molecular context to these protein structures, the models can be more easily appreciated in terms of function and structural integrity. Consequently, the AlphaFill models can be helpful in designing downstream wet-lab experiments and/or computational studies.

package alphafill

versions:

2.2.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libboost:

>=1.86.0,<1.87.0a0

depends libcifpp:

>=7.0.9,<8.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzeep:

>=6.1.1,<7.0a0

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 alphafill

and update with::

   mamba update alphafill

To create a new environment, run:

mamba create --name myenvname alphafill

with myenvname being 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/alphafill:<tag>

(see `alphafill/tags`_ for valid values for ``<tag>``)

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