NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.
Journal:
Nucleic acids research
PMID:
28407117
Abstract
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.
Authors
Keywords
Algorithms
Amino Acid Sequence
Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
Binding Sites
Cell Cycle Proteins
Databases, Protein
Forkhead Transcription Factors
HLA-A1 Antigen
HLA-B7 Antigen
HLA-B8 Antigen
HLA-DRB1 Chains
Humans
Internet
Ligands
Neural Networks, Computer
Peptides
Protein Binding
Sequence Alignment
Software
Trans-Activators