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Lewies A, Du Plessis LH, Wentzel JF. Antimicrobial Peptides: the Achilles’ Heel of Antibiotic Resistance? Probiotics Antimicrob Proteins 2018; 11:370-381. [DOI: 10.1007/s12602-018-9465-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Porto WF, Fensterseifer ICM, Ribeiro SM, Franco OL. Joker: An algorithm to insert patterns into sequences for designing antimicrobial peptides. Biochim Biophys Acta Gen Subj 2018; 1862:2043-2052. [PMID: 29928920 DOI: 10.1016/j.bbagen.2018.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/26/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
Innovative alternatives to control bacterial infections are need due to bacterial resistance rise. Antimicrobial peptides (AMPs) have been considered as the new generation of antimicrobial agents. Based on the fact that AMPs are sequence-dependent, a linguistic model for designing AMPs was previously developed, considering AMPs as a formal language with a grammar (patterns or motifs) and a vocabulary (amino acids). Albeit promising, that model has been poorly exploited mainly because thousands of sequences need to be generated, and the outcome has high similarity to already known AMPs. Here we present Joker, an innovative algorithm that improves the application of the linguistic model for rational design of antimicrobial peptides. We modelled the AMPs as a card game, where Joker combines the cards in the hand (patterns) with the cards in the table (sequence templates), generating a few variants. Our algorithm is capable of improving existing AMPs or even creating new AMPs from inactive peptides. A standalone version of Joker is available for download at <http://github.com/williamfp7/Joker> and requires a Linux 32-bit machine.
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Affiliation(s)
- William F Porto
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Porto Reports, Brasília, DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Isabel C M Fensterseifer
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil
| | - Suzana M Ribeiro
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, MS, Brazil
| | - Octavio L Franco
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil.
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