recipe usalign

Universal structure alignment of monomeric, complex proteins and nucleic acids

Homepage:

https://zhanggroup.org/US-align

Documentation:

https://zhanggroup.org/US-align/help

Developer docs:

https://github.com/pylelab/USalign

License:

OTHER / UNKNOWN

Recipe:

/usalign/meta.yaml

US-align (Universal Structural alignment) is a unified protocol to compare 3D structures of different macromolecules (proteins, RNAs and DNAs) in different forms (monomers, oligomers and heterocomplexes) for both pairwise and multiple structure alignments. The core alogrithm of US-align is extended from TM-align and generates optimal structural alignments by maximizing TM-score of compared strucures through heuristic dynamic programming iterations. Large-scale benchmark tests showed that US-align can generate more accurate structural alignments with significantly reduced CPU time, compared to the state-of-the-art methods developed for specific structural alignment tasks. TM-score has values in (0,1] with 1 indicating an identical structure match, where a TM-score ≥0.5 (or 0.45) means the structures share the same global topology for proteins (or RNAs).

package usalign

versions:

2024.07.30-0

depends libgcc:

>=12

depends libstdcxx:

>=12

requirements:

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 usalign

and update with::

   mamba update usalign

To create a new environment, run:

mamba create --name myenvname usalign

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/usalign:<tag>

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

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