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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;
  • Packages git and make

Download

Download biopep source code:

git clone https://github.com/lbqc-uesb/biopep.git

Installation

Navigate to biopep folder:

cd biopep

Give execution permission to scripts files

sudo chmod +x bin

Run installer script

make install

Run

Execute BioPep:

make run

Click here to see BioPep execution flow.

Options:

  • QUERY: query sequences file (.fasta, example: "/home/myuser/query.fasta") or pdb query folder (example: "/home/myuser/pdbs")
  • RECEPTOR: receptor file (.pdb, example: "/home/myuser/receptor.pdb")
  • SITE: binding site (example: "455:B, 486:B, 493:B, 501:B")
  • CUTOFF: max length of aminoacid sequence (default: 30)
  • TASK: taskname to save results folder (default: "task")

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.