AIMC Topic: Plant Proteins

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Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet.

International journal of biological macromolecules Jul 29, 2024
Drought stress is a major constraint on crop development, potentially causing huge yield losses and threatening global food security. Improving Crop's stress tolerance is usually associated with a yield penalty. One way to balance yield and stress to...
Computational Biology Setaria Plant Haplotypes Gene Expression Profiling Transcriptome Machine Learning Gene Expression Regulation, Plant Droughts Genes, Plant Plant Proteins Stress, Physiological
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Estimation of wheat protein content and wet gluten content based on fusion of hyperspectral and RGB sensors using machine learning algorithms.

Food chemistry Mar 22, 2024
The protein content (PC) and wet gluten content (WGC) are crucial indicators determining the quality of wheat, playing a pivotal role in evaluating processing and baking performance. Original reflectance (OR), wavelet feature (WF), and color index (C...
Triticum Plant Proteins Glutens Machine Learning Algorithms
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ASPTF: A computational tool to predict abiotic stress-responsive transcription factors in plants by employing machine learning algorithms.

Biochimica et biophysica acta. General subjects Mar 14, 2024
BACKGROUND: Abiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic ...
Plants Plant Proteins Gene Expression Regulation, Plant Machine Learning Algorithms Computational Biology Stress, Physiological Transcription Factors
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Deep learning-based characterization and redesign of major potato tuber storage protein.

Food chemistry Jan 23, 2024
Potato is one of the most important crops worldwide, to feed a fast-growing population. In addition to providing energy, fiber, vitamins, and minerals, potato storage proteins are considered as one of the most valuable sources of non-animal proteins ...
Plant Proteins Plant Tubers Carbohydrates Solanum tuberosum Deep Learning
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AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface.

Nature communications Sep 27, 2023
Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six def...
Endopeptidases Plant Diseases Peptide Hydrolases Plant Proteins Artificial Intelligence Solanum lycopersicum
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Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks.

BMC bioinformatics Jul 17, 2021
BACKGROUND: Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de novo from sequence is difficu...
Software Plant Proteins Neural Networks, Computer
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Predicting functions of maize proteins using graph convolutional network.

BMC bioinformatics Dec 16, 2020
BACKGROUND: Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are annotated using the Gene Ont...
Zea mays Neural Networks, Computer Gene Ontology Humans Molecular Sequence Annotation Plant Proteins Area Under Curve
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Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes.

PloS one Jun 19, 2020
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC...
Databases, Genetic Oryza Signal Transduction Diploidy Plant Proteins Gene Duplication Gene Ontology Genome, Plant Vitis Arabidopsis Multigene Family
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Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction.

Genomics May 11, 2020
Long non-coding RNAs (lncRNAs) play key roles in regulating cellular biological processes through diverse molecular mechanisms including binding to RNA binding proteins. The majority of plant lncRNAs are functionally uncharacterized, thus, accurate p...
RNA-Binding Proteins RNA, Long Noncoding Plant Proteins Arabidopsis Zea mays Deep Learning RNA, Plant
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JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.

BMC genomics Dec 24, 2019
BACKGROUND: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energ...
Models, Biological Jatropha Gene Regulatory Networks Knowledge Bases Software Genomics Plant Proteins Gene Expression Profiling Protein Interaction Mapping Genes, Plant
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