ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence ProNA2020 can predict protein-DNA, protein-RNA and protein-protein binding sites with only sequence information. It is a two level prediction. In first level, ProNA2020 will predict whether the input protein is a binding protein. If the input protein is a binding protein, then ProNA2020 will give the residue level prediction.
After downloading, you need install some necessary python package and sofware before you use ProNA2019.
pybrain (>=0.3.3)
scikit-learn (=0.19.1-2)
botocore (>=1.10.33)
smart-open (>=1.5.7)
ncbi-blast+
fastprofkernel (>=1.0.24)
Usage: prona2020 [options]
Options:
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-h:show this help message and exit
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-p:PATH,Directory containing the PredictProtein output files with the suffixes .chk .in .fasta .blastPsiMat .profbval .mdisorder and .profRdb.
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-o:FILENAME,Output file. If not specified, the output is written to STDOUT.
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-l:LABEL,Turn off protein level prediction by inputting binding label, e.g. "-l Protein_DNA", which means the input protein is already known as a Protein- and DNA-binding protein.
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-d:DATABASE,Use your own local database for PSI-BLAST (homology based inference), default is using the profile (.chk) from big_80 database(rostlab) which is a comprehensive blast database at 80% sequence identity redundancy level
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-v:Print verbose or not (True/False), default is False