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PoonLab / tuning-disorder-virus

Ensemble classifier of intrinsic protein disorder for viruses
MIT License
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Software Licensure #1

Closed Abayomi-Olabode closed 3 years ago

Abayomi-Olabode commented 4 years ago

Seems we need to email the software creators before re-distributing them.

IUPred2a

https://iupred2a.elte.hu/license_new

Spot-Disorder2

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Hello user,
Thank you for your interest in our predictor. SPOT-Disorde2 requires 
several python (2.7) packages, please verify that they are installed before use:

    tensorflow (v1.10)    ---> see https://www.tensorflow.org/install/
    numpy
    tqdm
    cPickle

It also requires SPIDER3, SPOT-1D, SPOT-Contact, PSI-BLAST, and HHBlits
for prediction from the protein fasta/sequence files. Please ensure this are 
installed and in working order. Please also ensure that the SPOT-Contact SS 
probabilities are in the range of [0-1] (this was changed in early versions).

PLEASE EDIT THE FILEPATHS IN "run_spotdis2.sh" BEFORE RUNNING TO THE CORRECT 
LOCATIONS.

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USAGE:
To run for a sample protein, please place all already-completed files (.spotcon,
.fasta, .hhm, .pssm, .spot1d) into the "input" directory and run:

    ./run_spotdis2.sh 

The minimum needed is a fasta file. This code will skip the file creation if the
required file can be found. This is particularly useful if you already have 
generated your evolutionary profiles or the SPOT-Contact outputs, as these take 
the longest by far.

This commend generates all files needed for SPOT-Disorder2, and will also
 generate an input list called "protlist.txt" which will be used by the program 
"run_all_models.py". If you only want to run over some models, please create and
use your own "protlist.txt".

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PLEASE CITE!:
If you use this predictor in your research, please cite:

Hanson, J., Paliwal, K., Litfin, T., and Zhou, Y., Enhancing Protein Intrinsic Disorder Prediction by Utilizing Deep Squeeze and Excitation Residual Inception and Long Short-Term Memory Networks, 2018

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Thanks again!
Jack Hanson and the Sparks-lab team
ArtPoon commented 3 years ago

We decided not to redistribute binaries, but we should make these package dependencies.