lucian-ilie/PITHIA

PITHIA: Protein interaction site prediction using multiple sequence alignments and attention

The source code of PITHIA

The PITHIA source code is designed for high-throughput prediction. It does not have the limitation of 10 sequences per run.

Web server

PITHIA is freely available as a web server at http://pithia.csd.uwo.ca/.

Citation

S. Hosseini, L. Ilie, PITHIA: protein interaction site prediction using multiple sequence alignments and attention, International Journal of Molecular Sciences 23(21) (2022) 12814.

Contact:

SeyedMohsen Hosseini (shosse59@uwo.ca) Lucian Ilie (ilie@uwo.ca)

System requirement

PITHIA is developed under Linux environment with python 3.7. Recommended RAM: > 24GB. The RAM requirement mainly depends on the length of the input sequence.

Installation

1. clone the source code of PITHIA

mkdir -p Src && cd Src
git clone [PITHIA git link]

2. install python packages. Python virtual environment is recommended for package management.

pip3 install -r requirement.txt

3. install dependencies

• install hh-suite. The database used in PITHIA is uniref30_2020_06.

Running PITIHA

bash run_PITIHA.sh [Fasta file]