recipe psipred

Protein Secondary Structure Predictor

Homepage:

https://bioinf.cs.ucl.ac.uk/psipred

Documentation:

https://github.com/psipred/psipred/blob/v4.0/README

Developer docs:

https://github.com/psipred/psipred

License:

OTHER / CUSTOM (academic-only)

Recipe:

/psipred/meta.yaml

Links:

doi: 10.1006/jmbi.1999.3091

PSIPRED is a simple and accurate secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from [PSI-BLAST](http://www.ncbi.nlm.nih.gov/blast) (Position Specific Iterated - BLAST). Using a very stringent cross validation method to evaluate the method's performance, PSIPRED 3.2 achieves an average Q3 score of 81.6%. Predictions produced by PSIPRED were also submitted to the [CASP4](http://predictioncenter.llnl.gov/casp4/) evaluation and assessed during the CASP4 meeting, which took place in December 2000 at Asilomar. PSIPRED 2.0 achieved an average Q3 score of 80.6% across all 40 submitted target domains with no obvious sequence similarity to structures present in PDB, which ranked PSIPRED top out of 20 evaluated methods (an earlier version of PSIPRED was also ranked top in CASP3 held in 1998). It is important to realise, however, that due to the small sample sizes, the results from CASP are not statistically significant, although they do give a rough guide as to the current "state of the art". For a more reliable evaluation, the [EVA](http://pdg.cnb.uam.es/eva/) web site at Columbia University provides a continuous evaluation. NOTE that at the time of writing, the EVA site is no longer being updated. Downloads: The PSIPRED V3.2 software can be downloaded from [HERE](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/). Please note that you should read the license terms given in the [README](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README) file if you wish to incorporate PSIPRED in another program or Web server. Older releases of PSIPRED can be downloaded here [HERE](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/).

package psipred

(downloads) docker_psipred

versions:

4.0-0,  3.5-0

depends blast-legacy:

depends libgcc:

>=13

depends tcsh:

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 psipred

and update with::

   mamba update psipred

To create a new environment, run:

mamba create --name myenvname psipred

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/psipred:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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/psipred/README.html)