Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Privacy-aware community infrastructureResearch graph
References from GeoEPred: A multimodal structure-aware geometric deep learning framework for Gram-negative bacterial secreted effector prediction with sequence semantics. Local targets link to admitted publications; unresolved targets remain external evidence.
Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID)
10.1038/s42003-025-07950-y · 2025 · External reference
Bacterial protein secretion systems: Mechanisms, functions, and roles in virulence
10.1016/j.micpath.2025.107790 · 2025 · External reference
The type VI secretion system and associated effector proteins
10.1038/s41579-025-01256-w · 2026 · External reference
Microbial adaptive pathogenicity strategies to the host inflammatory environment
2025 · External reference
Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions
10.1074/mcp.m000027-mcp201 · 2010 · External reference
Identification of a Novel Salmonella Type III Effector by Quantitative Secretome Profiling
10.1074/mcp.ra117.000230 · 2017 · External reference
Bastion3: a two-layer ensemble predictor of type III secreted effectors
10.1093/bioinformatics/bty914 · 2019 · External reference
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors
10.1093/bioinformatics/bty155 · 2018 · External reference
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery
10.1093/bib/bbz120 · 2020 · External reference
An account of in silico identification tools of secreted effector proteins in bacteria and future challenges
10.1093/bib/bbx078 · 2019 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
10.1073/pnas.2016239118 · 2021 · External reference
DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria
2023 · External reference
MoCETSE: A mixture-of-convolutional experts and transformer-based model for predicting Gram-negative bacterial secreted effectors
2026 · External reference
Protein sectors: evolutionary units of three-dimensional structure
10.1016/j.cell.2009.07.038 · 2009 · External reference
Learning spatial structures of proteins improves protein-protein interaction prediction
10.1093/bib/bbab558 · 2022 · External reference
Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction
2023 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
10.1038/s41564-022-01287-6 · 2023 · External reference
Phytopathogen Effector Biology in the Burgeoning AI Era
10.1146/annurev-phyto-121823-081033 · 2025 · External reference
TSE-ARF: An adaptive prediction method of effectors across secretion system types
10.1016/j.ab.2023.115407 · 2024 · External reference
DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence
10.1093/bioinformatics/bty931 · 2019 · External reference
SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems
10.1007/s11427-022-2172-x · 2023 · External reference
DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors
10.3389/fmicb.2021.605782 · 2021 · External reference
Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool
10.3389/fmicb.2019.01391 · 2019 · External reference
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model
10.1093/bib/bbab420 · 2022 · External reference
iT4SE-EP: Accurate Identification of Bacterial Type IV Secreted Effectors by Exploring Evolutionary Features from Two PSI-BLAST Profiles
10.3390/molecules26092487 · 2021 · External reference
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches
10.1093/bib/bbx164 · 2019 · External reference
T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm
10.3389/fmicb.2020.580382 · 2020 · External reference
10.1016/j.csbj.2024.01.015 · 2024 · Admitted local publication
Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles
10.1093/bioinformatics/btt554 · 2013 · External reference
Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini
10.1007/s10822-017-0080-z · 2017 · External reference
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
10.1093/bioinformatics/btl158 · 2006 · External reference
SignalP 6.0 predicts all five types of signal peptides using protein language models
10.1038/s41587-021-01156-3 · 2022 · External reference
Large language models generate functional protein sequences across diverse families
10.1038/s41587-022-01618-2 · 2023 · External reference
Unresolved reference
External reference
MDbDMRP: A novel molecular descriptor-based computational model to identify drug-miRNA relationships
10.1016/j.ijbiomac.2024.138580 · 2025 · External reference
Uniform manifold approximation and projection
10.1038/s43586-024-00363-x · 2024 · External reference
Opportunities and challenges in design and optimization of protein function
10.1038/s41580-024-00718-y · 2024 · External reference
The relation between the divergence of sequence and structure in proteins
10.1002/j.1460-2075.1986.tb04288.x · 1986 · External reference
How significant is a protein structure similarity with TM-score = 0.5?
10.1093/bioinformatics/btq066 · 2010 · External reference
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria
2021 · External reference
T1SEstacker: A Tri-Layer Stacking Model Effectively Predicts Bacterial Type 1 Secreted Proteins Based on C-Terminal Non-repeats-in-Toxin-Motif Sequence Features
10.3389/fmicb.2021.813094 · 2021 · External reference
T3SEpp: an integrated prediction pipeline for bacterial type III secreted effectors
2020 · External reference
Features and algorithms: facilitating investigation of secreted effectors in Gram-negative bacteria
10.1016/j.tim.2023.05.011 · 2023 · External reference
Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2
10.1007/978-1-0716-3445-5_1 · 2024 · External reference
Type VI Secretion Effectors: Methodologies and Biology
10.3389/fcimb.2017.00254 · 2017 · External reference
LpnE is a Legionella pneumophila virulence factor required for efficient invasion of host cells
2007 · External reference
The ADP-Ribosyltransferase Domain of the Effector Protein ExoS from Pseudomonas aeruginosa
2014 · External reference
GAP activity of the Yersinia YopE cytotoxin specifically targets the Rho pathway: a mechanism for disruption of actin microfilament structure
10.1046/j.1365-2958.2000.01898.x · 2000 · External reference
Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin
10.1073/pnas.0813360106 · 2009 · External reference
PyMOL: an open-source molecular graphics tool
2002 · External reference
A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium
10.1073/pnas.97.13.7539 · 2000 · External reference
Crystal structures of two bacterial HECT-like E3 ligases in complex with E2 enzymes
2012 · External reference
The structure of the SlrP–Trx1 complex sheds light on the autoinhibition mechanism of the type III secretion system effectors of the NEL family
10.1042/bj20140587 · 2014 · External reference
Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ
10.7554/elife.51162 · 2019 · External reference
Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation
10.1038/s41586-019-1440-8 · 2019 · External reference
Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase
10.1038/s41586-019-1439-1 · 2019 · External reference
Structural and mechanistic basis for protein glutamylation by the kinase fold
10.1016/j.molcel.2021.08.007 · 2021 · External reference
Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane
10.1038/s41467-023-43585-5 · 2023 · External reference
Computational prediction of secreted proteins in gram-negative bacteria
10.1016/j.csbj.2021.03.019 · 2021 · External reference
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions
10.1016/s0022-2836(02)00649-6 · 2002 · External reference
Cytotoxicity induced by Aeromonas schubertii is orchestrated by a unique set of type III secretion system effectors
10.1186/s13567-025-01548-2 · 2025 · External reference
A new class of type VI secretion system effectors can carry two toxic domains and are recognized through the WHIX motif for export
10.1371/journal.pbio.3003053 · 2025 · External reference
Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas
10.3389/fpls.2023.1155341 · 2023 · External reference
Role of Type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection
10.1093/ismejo/wrae053 · 2024 · External reference
