Open AccessPeptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach
Author(s) -
Cristofer Quiroz,
Yasna Barrera Saavedra,
Benjamín Armijo-Galdames,
Juan Amado-Hinojosa,
Álvaro Olivera-Nappa,
Anamaria Sanchez-Daza,
David Medina-Ortiz
Publication year - 2021
Publication title -
database
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.406
H-Index - 62
ISSN - 1758-0463
DOI - 10.1093/database/baab055
Subject(s) - computer science , usability , database , user friendly , software , biological database , source code , world wide web , web application , bioinformatics , human–computer interaction , biology , programming language , operating system
Peptides have attracted attention during the last decades due to their extraordinary therapeutic properties. Different computational tools have been developed to take advantage of existing information, compiling knowledge and making available the information for common users. Nevertheless, most related tools available are not user-friendly, present redundant information, do not clearly display the data, and usually are specific for particular biological activities, not existing so far, an integrated database with consolidated information to help research peptide sequences. To solve these necessities, we developed Peptipedia, a user-friendly web application and comprehensive database to search, characterize and analyse peptide sequences. Our tool integrates the information from 30 previously reported databases with a total of 92 055 amino acid sequences, making it the biggest repository of peptides with recorded activities to date. Furthermore, we make available a variety of bioinformatics services and statistical modules to increase our tool's usability. Moreover, we incorporated a robust assembled binary classification system to predict putative biological activities for peptide sequences. Our tools' significant differences with other existing alternatives become a substantial contribution for developing biotechnological and bioengineering applications for peptides. Peptipedia is available for non-commercial use as an open-access software, licensed under the GNU General Public License, version GPL 3.0. The web platform is publicly available at peptipedia.cl. Database URL: Both the source code and sample data sets are available in the GitHub repository https://github.com/ProteinEngineering-PESB2/peptipedia.