NNAlign: a platform to construct and evaluate artificial neural network models of receptor–ligand interactions

 

Autores
Nielsen, Morten; Andreatta, Massimo
Tipo de recurso
artículo
Estado
Versión publicada
Año de publicación
2017
País
Argentina
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio
CONICET Digital (CONICET)
Descripción
Peptides are extensively used to characterize functional or (linear) structural aspects of receptor–ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and phosphatases. NNAlign is a method for the identification of such linear motifs in biological sequences. The algorithm aligns the amino acid or nucleotide sequences provided as training set, and generates a model of the sequence motif detected in the data. The webserver allows setting up cross-validation experiments to estimate the performance of the model, as well as evaluations on independent data. Many features of the training sequences can be encoded as input, and the network architecture is highly customizable. The results returned by the server include a graphical representation of the motif identified by the method, performance values and a downloadable model that can be applied to scan protein sequences for occurrence of the motif. While its performance for the characterization of peptide–MHC interactions is widely documented, we extended NNAlign to be applicable to other receptor–ligand systems as well. Version 2.0 supports alignments with insertions and deletions, encoding of receptor pseudo-sequences, and custom alphabets for the training sequences. The server is available at http://www.cbs.dtu.dk/services/NNAlign-2.0.
Idioma
inglés
OAI Identifier
oai:ri.conicet.gov.ar:11336/48716
Enlace del recurso
http://hdl.handle.net/11336/48716
Nivel de acceso
Acceso abierto
Materia
RECEPTOR-LIGAND INTERACTION
ARTIFICIAL NEURAL NETWORK
SEQUENCE ALIGNMENT
MACHINE LEARNING
Ciencias de la Computación
Ciencias de la Computación e Información
CIENCIAS NATURALES Y EXACTAS