Package Recipe 'alphafill'

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:

2.3.0-0, 2.2.0-0

Depends:

on bzip2 >=1.0.8,<2.0a0
on howardhinnant_date >=3.0.4,<3.1.0a0
on libboost >=1.88.0,<1.89.0a0
on libcifpp >=9.0.4,<10.0a0
on libgcc >=14
on libstdcxx >=14
on libzeep >=7.3.1,<8.0a0
on libzlib >=1.3.1,<2.0a0
on mxml >=2.0.4,<2.0.5.0a0

Additional platforms:

linux-aarch64, osx-arm64

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 alphafill

to add into an existing workspace instead, run:

pixi add alphafill

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 alphafill

Alternatively, to install into a new environment, run:

conda create -n envname alphafill

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/alphafill:<tag>

(see alphafill/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/alphafill/README.html)