BioPep

Pipeline for the search of homologues and molecular modeling for each peptide as well as the molecular docking between the peptides and the RBD receptor (PDB: 6LZG) of SARS-CoV-2.

By Lucas Palmeira: CNPq Technological Initiation Scholarship | Data Scientist in Training
By William Sena: CNPq Technological Initiation Scholarship | Python Developer

Licence

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007

Requisites

• A Modeller License Key;
• System Operational with Docker installed;

Installation

After to clone this repository, navigate to project folder:

cd biopep

Copy .env file and add the Modeller KEY:

cp .env.example .env

Up containers:

docker compose up -d

Run

Access BioPep container shell:

docker exec -it biopep bash

Activate conda environment:

eval "$(conda shell.bash hook)" && conda activate biopep-env

Execute BioPep:

python main.py query.fasta taskname

query.fasta: file with peptides for submit
taskname: title to your task, for save in output folder

Please, cite:

BioPep

Lucas Sousa Palmeira, & William Sena. (2021). BioPep. Zenodo. https://doi.org/10.5281/zenodo.5781778

Hpepdock:

ZHOU, Pei; JIN, Bowen; LI, Hao; et al. HPEPDOCK: A web server for blind peptide-protein acoplamento based on a hierarchical algorithm. Nucleic Acids Research, v. 46, n. W1, p. W443–W450, 2018.

Modeller:

ŠALI, Andrej; BLUNDELL, Tom L. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, v. 234, n. 3, p. 779–815, 1993.

WEBB, Benjamin; SALI, Andrej. Comparative Protein Structure Modeling Using MODELLER. Current protocols in bioinformatics, v. 54, p. 5.6.1-5.6.37, 2016.

Blast:

CAMACHO, Christiam; COULOURIS, George; AVAGYAN, Vahram; et al. BLAST+: architecture and applications. BMC Bioinformatics, v. 10, p. 421, 2009.

APD3: The antimicrobial peptide database

WANG, Guangshun; LI, Xia; WANG, Zhe. APD3: The antimicrobial peptide database as a tool for research and education. Nucleic Acids Research, v. 44, n. D1, p. D1087–D1093, 2016.