SignalP 6.0 predicts all five types of signal peptides using protein language models

2022/01/03 by Felix Teufel, José Juan Almagro Armenteros, Alexander Rosenberg Johansen +7 · 77 citations
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Machine Learning in Bioinformatics #vaccines and immunoinformatics approaches

paper · pdf · doi:10.1038/s41587-021-01156-3

openalex publication_date 2022/01/03 · openalex created_date 2022/01/26 · openalex updated_date 2026/07/31

Abstract

Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.

Citations

• A simple method for displaying the hydropathic character of a protein
• Pfam: The protein families database in 2021
• Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
• ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning

Cited by

• On the dynamic caddisfly silk <i>H-fibroin</i> gene: a population study in a net-spinning species
• Plastic degradation by enzymes from uncultured deep sea microorganisms
• Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I
• Reverse vaccinology for hookworms: a rational selection of vaccinable antigens against parasitic nematodes
• Neuropeptide Diversity Encoded in Newly Sequenced Crustacean Genomes Reveals Signaling Roles during Feeding
• Evolutionary innovation within conserved gene regulatory networks underlying biomineralized skeletons in Bilateria
• Ageing promotes microglial accumulation of slow-degrading synaptic proteins
• Analysis of protease production in the microbial antagonist <i>Pythium oligandrum</i> and host/prey <i>Pythium myriotylum</i> protease inhibitors
• Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci
• Temporal Dynamics of Gene Expression During Metamorphosis in Two Distant <i>Drosophila S</i> pecies
• Proteomic analyses reveal the key role of gene co-option in the evolution of the scaly-foot snail scleritome
• Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures
• Functional diversification of a wild potato immune receptor at its center of origin
• CCDC134 controls TLR biogenesis through the ER chaperone Gp96
• Functional divergence and structural changes of Class IV histone deacetylases (HDACs) across the tree of life
• Emerging technologies for the discovery of biosynthetic genes in plants
• Finding functional motifs in protein sequences with deep learning and natural language models
• InterPro in 2022
• Sketching microprotein portraits
• The ancient E-ring in bacterial flagellar motors
• Guiding questions to avoid data leakage in biological machine learning applications
• Genomic investigations in animal enteric disease-associated Clostridium perfringens
• The degradation of glycosaminoglycans by haloarchaea is apparently a common feature in hypersaline habitats worldwide
• Microbial <scp>dl</scp> -Peptidases Enable Predator Defense and Facilitate Structure Elucidation of Complex Natural Products
• Invasive Acinetobacter baumannii ABC141 strain relies on the twin-arginine translocation export system for adhesion to host cells
• Genome mining of amylases and amylase inhibitors from Streptomyces
• Beyond venomous fangs: Uloboridae spiders have lost their venom but not their toxicity
• A Broad Genome Survey Reveals Widespread Presence of Secretoglobin Genes in Squamate and Archosaur Reptiles that Flowered into Diversity in Mammals
• Are protein language models the new universal key?
• A type II secreted subtilase from commensal rhizobacteria cleaves immune elicitor peptides and suppresses flg22-induced immune activation
• Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents
• Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil
• Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam
• Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility
• Lifestyles shape genome size and gene content in fungal pathogens
• Molecular dynamics of the matrisome across sea anemone life history
• A new paradigm for outer membrane protein biogenesis in the Bacteroidota
• Purification and characterization of a novel antibacterial peptide against Clostridium perfringens
• Origin and Evolution of Bacterial Periplasmic Force Transducers
• Mapping the ultrastructural topology of the corynebacterial cell surface
• Mapping the ultrastructural topology of the corynebacterial cell surface
• Degradation Behavior of Aliphatic–Aromatic Polyesters: from Microplastic-free Composting to Enzyme-Driven Recycling Possibility
• C‐terminal anchor endolysins—proposing a third class of tailed bacteriophage endolysins
• Haptophyte-infecting viruses change the genome condensing proteins of dinoflagellates
• Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model
• The Molecular Dialogue Between <i>Zymoseptoria tritici</i> and Wheat
• Codon language embeddings provide strong signals for protein engineering
• DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks
• <scp> S ² </scp> ‐ <scp>PepAnalyst</scp> : A Web Tool for Predicting Plant Small Signalling Peptides
• Structural and Transcriptional Diversity in the Repertoire of <i>Sclerotinia sclerotiorum</i> Effector Candidates
• Comparative Genomics Provide Insight Into the Evolution of European <i>Aphanomyces euteiches</i> Strains
• Draft Genome Sequence Resource of the Citrus Greasy Spot Fungal Pathogen <i>Zasmidium citri-griseum</i> Isolate MCC3
• Exploring the lipoproteome of Parageobacillus thermoglucosidasius
• Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid <i>Platynereis dumerilii</i>
• An RGAE Homolog in <i>Fusarium graminearum</i> Is Critical for Initial Infection in Wheat and Barley
• Rapid Identification of Superior Endogenous Signal Peptides for Heterologous Protein Secretion by <scp> <i>Corynebacterium glutamicum</i> </scp> Through Modular Cloning and Automation
• The SPARK complex forms the molecular basis of vertebrate fertilization
• Understanding the substrate recognition and catalytic mechanism of 2-O-methyl fucosidases from glycoside hydrolase family 139
• An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota
• Massive experimental quantification allows interpretable deep learning of protein aggregation
• Functional diversification of dietary plant small molecules by the gut microbiome
• Localization of heme biosynthesis in the diatom Phaeodactylum tricornutum and differential expression of multi-copy enzymes
• Optimizing protein tokenization: reduced amino acid alphabets for efficient and accurate protein language models
• Distinguishing <i>Leptothrix</i> and <i>Sphaerotilus</i> genera by an integrated genomic-phenotypic analysis supported by new <i>Leptothrix</i> genomes
• Genome Resource of Representative Isolates of <i>Fusarium solani</i> and <i>Fusarium falciforme</i> Pathogenic on Soybean
• Characterization of Two <i>Salmonella</i> Myoviruses and a Novel Lysis-Inhibition System
• iMFP-LG: Identify Novel Multi-functional Peptides Using Protein Language Models and Graph-based Deep Learning
• AtNHR2A and AtNHR2B: Two Players of the Plant Secretory Pathway Functioning in Biotic Stress Responses
• HPClas: A data‐driven approach for identifying halophilic proteins based on catBoost
• Food production from air: gas precision fermentation with hydrogen-oxidising bacteria
• Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria
• Evolution of Highly Repetitive Silk Genes in the Luna Moth, <i>Actias luna</i>
• Genomic and physiological signatures of adaptation in pathogenic fungi
• Winter‐active spiders ( <i>Clubiona</i> ) have a hyperactive antifreeze protein with a unique beta‐solenoid fold
• Gene duplication drove functional divergence of two effectors in the maize anthracnose pathogen
• A third type of <scp>PETase</scp> from the marine <i>Halopseudomonas</i> lineage
• TropiCODB: A multi-omics resource for supporting biodesign in tropical crops

Related

• SignalP 6.0 predicts all five types of signal peptides using protein language models
• Machine Learning for Protein Function
• Combined Genome and Protein Statistical Features Improved the Prediction of Genes Encoding Antimicrobial Peptides: A Machine Learning Based Approach
• Finding functional motifs in protein sequences with deep learning and natural language models
• Discovery of Proteomics based on Machine learning