- recipe usalign
Universal structure alignment of monomeric, complex proteins and nucleic acids
- Homepage:
- Documentation:
- Developer docs:
- License:
OTHER / UNKNOWN
- Recipe:
- Links:
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:
20241201-0,2024.07.30-1,2024.07.30-0- Depends:
on libgcc
>=13on libstdcxx
>=13
- 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 usalign
to add into an existing workspace instead, run:
pixi add usalign
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 usalign
Alternatively, to install into a new environment, run:
conda create -n envname usalign
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/usalign:<tag>
(see usalign/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/usalign/README.html)
