Structure-aware machine learning strategies for antimicrobial peptide discovery.
Sci Rep
; 14(1): 11995, 2024 05 25.
Article
en En
| MEDLINE
| ID: mdl-38796582
ABSTRACT
Machine learning models are revolutionizing our approaches to discovering and designing bioactive peptides. These models often need protein structure awareness, as they heavily rely on sequential data. The models excel at identifying sequences of a particular biological nature or activity, but they frequently fail to comprehend their intricate mechanism(s) of action. To solve two problems at once, we studied the mechanisms of action and structural landscape of antimicrobial peptides as (i) membrane-disrupting peptides, (ii) membrane-penetrating peptides, and (iii) protein-binding peptides. By analyzing critical features such as dipeptides and physicochemical descriptors, we developed models with high accuracy (86-88%) in predicting these categories. However, our initial models (1.0 and 2.0) exhibited a bias towards α-helical and coiled structures, influencing predictions. To address this structural bias, we implemented subset selection and data reduction strategies. The former gave three structure-specific models for peptides likely to fold into α-helices (models 1.1 and 2.1), coils (1.3 and 2.3), or mixed structures (1.4 and 2.4). The latter depleted over-represented structures, leading to structure-agnostic predictors 1.5 and 2.5. Additionally, our research highlights the sensitivity of important features to different structure classes across models.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Aprendizaje Automático
/
Péptidos Antimicrobianos
Idioma:
En
Revista:
Sci Rep
Año:
2024
Tipo del documento:
Article
País de afiliación:
México