The web server of Porter 5 is available at http://distilldeep.ucd.ie/porter/.
The train and test sets are available at http://distilldeep.ucd.ie/porter/data/.
More protein structure annotation predicted at http://distilldeep.ucd.ie/brewery/.
Porter 5: fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
Mirko Torrisi, Manaz Kaleel and Gianluca Pollastri; bioRxiv 289033; doi: https://doi.org/10.1101/289033.
$ git clone https://github.com/mircare/Porter5/
or
$ wget http://distilldeep.ucd.ie/porter/data/Porter5.tgz
$ tar zxvf Porter5.tgz
- Python3 (https://www.python.org/downloads/);
- NumPy (https://www.scipy.org/scipylib/download.html);
- HHblits (https://github.com/soedinglab/hh-suite/);
- uniprot20 (http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/uniprot20_2016_02.tgz).
- PSI-BLAST (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/);
- UniRef90 (ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz).
# To exploit HHblits only (for fast and accurate predictions)
$ python3 Porter5/Porter5.py -i Porter5/example/2FLGA.fasta --cpu 4 --fast
# To exploit both PSI-BLAST and HHblits (for very accurate predictions)
$ python3 Porter5/Porter5.py -i Porter5/example/2FLGA.fasta --cpu 4
| Method | Q3 per AA | SOV'99 per AA | Q3 per protein | SOV'99 per protein |
|---|---|---|---|---|
| Porter 5 | 83.81% | 80.41% | 84.32% | 81.05% |
| SPIDER 3 | 83.15% | 79.43% | 83.42% | 79.79% |
| Porter 5 HHblits only | 83.06% | 79.49% | 83.68% | 80.26% |
| SSpro 5 with templates | 82.58% | 78.54% | 83.94% | 80.29% |
| PSIPRED 4.01 | 81.88% | 77.36% | 82.48% | 78.22% |
| RaptorX-Property | 81.86% | 78.08% | 82.57% | 78.99% |
| Porter 4 | 81.66% | 78.05% | 82.29% | 78.61% |
| SSpro5 ab initio | 81.17% | 76.87% | 81.10% | 76.92% |
| DeepCNF | 81.04% | 76.74% | 81.16% | 76.99% |
Calculated with http://dna.cs.miami.edu/SOV/.
| Method | Q8 per AA | SOV8'99 per AA | Q8 per protein | SOV8'99 per protein |
|---|---|---|---|---|
| Porter5 | 73.02% | 69.91% | 73.92% | 70.76% |
| SSpro 5 with templates | 71.91% | 68.68% | 74.46% | 71.74% |
| Porter5 HHblits only | 71.8% | 68.87% | 72.83% | 69.79% |
| RaptorX-Property | 70.74% | 67.59% | 71.78% | 68.36% |
| DeepCNF | 69.76% | 66.42% | 70.14% | 66.44% |
| SSpro5 ab initio | 68.85% | 65.33% | 69.27% | 65.97% |
Calculated with http://dna.cs.miami.edu/SOV/.
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Email us at gianluca[dot]pollastri[at]ucd[dot]ie if you wish to use it for purposes not permitted by the CC BY-NC-SA 4.0.
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