AIMC Topic: Fungal Proteins

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EffectorP: predicting fungal effector proteins from secretomes using machine learning.

The New phytologist Dec 17, 2015
Eukaryotic filamentous plant pathogens secrete effector proteins that modulate the host cell to facilitate infection. Computational effector candidate identification and subsequent functional characterization delivers valuable insights into plant-pat...
Amino Acids Molecular Weight Fungal Proteins Species Specificity Fusarium Algorithms Reproducibility of Results Computational Biology Machine Learning Cytoplasm Genome, Fungal
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mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.

Database : the journal of biological databases and curation Mar 8, 2015
Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and...
Enzymes Databases, Genetic Natural Language Processing Fungal Proteins Data Mining Genes, Fungal Lignin Data Curation
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ActiMut-XGB: Predicting thermodynamic stability of point mutations for CALB with protein language model.

International journal of biological macromolecules Jun 1, 2025
Predicting the functional impact of single-point mutations on protein residual activity, especially after high-temperature incubation, is critical in protein engineering. We present an innovative machine learning model based on eXtreme Gradient Boost...
Protein Engineering Machine Learning Models, Molecular Enzyme Stability Fungal Proteins Thermodynamics Lipase Point Mutation
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DeepMBEnzy: An AI-Driven Database of Mycotoxin Biotransformation Enzymes.

Journal of agricultural and food chemistry May 28, 2025
Mycotoxins are toxic fungal metabolites that pose significant health risks. Enzyme biotransformation is a promising option for detoxifying mycotoxins and for elucidating their intracellular metabolism. However, few mycotoxin-biotransformation enzymes...
Enzymes Biotransformation Fungal Proteins Mycotoxins Databases, Factual Fungi Deep Learning
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Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks.

Bioinformatics (Oxford, England) Jul 11, 2022
MOTIVATION: Phytopathogenic fungi secrete effector proteins to subvert host defenses and facilitate infection. Systematic analysis and prediction of candidate fungal effector proteins are crucial for experimental validation and biological control of ...
Fungal Proteins Machine Learning Computational Biology
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Machine learning for phytopathology: from the molecular scale towards the network scale.

Briefings in bioinformatics Sep 2, 2021
With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within...
Plants Plant Diseases Gene Expression Regulation Bacterial Proteins NLR Proteins Viral Proteins Protein Interaction Mapping Disease Resistance Fungal Proteins Host-Pathogen Interactions Protein Serine-Threonine Kinases Bayes Theorem Support Vector Machine Receptors, Pattern Recognition Pathogen-Associated Molecular Pattern Molecules Plant Pathology
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DiagnoProt: a tool for discovery of new molecules by mass spectrometry.

Bioinformatics (Oxford, England) Jun 15, 2017
MOTIVATION: Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortli...
Fungal Proteins Sequence Analysis, Protein Proteomics Aspergillus Tandem Mass Spectrometry Machine Learning Software
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Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix.

Oncotarget Dec 13, 2016
Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interact...
Principal Component Analysis Humans Fungal Proteins Computational Biology Databases, Protein Sequence Analysis, Protein Protein Interaction Mapping Support Vector Machine Position-Specific Scoring Matrices
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[Gene optimization and efficient expression of Trichoderma reesei Cel5A in Pichia pastoris].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Oct 25, 2016
Deficient activity of endo-1,4-beta-glucanase II (Cel5A) secreted by Trichoderma reesei is one of the challenges involved in effective cellulase saccharification of cellulosic substrates. Therefore, we expressed Cel5A in Pichia pastoris by constructi...
Trichoderma Cellulose 1,4-beta-Cellobiosidase Codon Fermentation Cellulose Temperature Gene Expression Fungal Proteins Recombinant Proteins Pichia Industrial Microbiology Gentamicins Cellulase
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