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1. Dockground resource for protein recognition studies

   https://doi.org/10.1002/pro.4481  

   Collins, Keeley W.; Copeland, Matthew M.; Kotthoff, Ian; Singh, Amar; Kundrotas, Petras J.; Vakser, Ilya A. (December 2022, Protein Science)

   Abstract Structural information of protein–protein interactions is essential for characterization of life processes at the molecular level. While a small fraction of known protein interactions has experimentally determined structures, computational modeling of protein complexes (protein docking) has to fill the gap. TheDockgroundresource (http://dockground.compbio.ku.edu) provides a collection of datasets for the development and testing of protein docking techniques. Currently,Dockgroundcontains datasets for the bound and the unbound (experimentally determined and simulated) protein structures, model–model complexes, docking decoys of experimentally determined and modeled proteins, and templates for comparative docking. TheDockgroundbound proteins dataset is a core set, from which otherDockgrounddatasets are generated. It is devised as a relational PostgreSQL database containing information on experimentally determined protein–protein complexes. This report on theDockgroundresource describes current status of the datasets, new automated update procedures and further development of the core datasets. We also present a newDockgroundinteractive web interface, which allows search by various parameters, such as release date, multimeric state, complex type, structure resolution, and so on, visualization of the search results with a number of customizable parameters, as well as downloadable datasets with predefined levels of sequence and structure redundancy. 

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2. ProTaxoVis—protein taxonomic visualisation of presence

   https://doi.org/10.1186/s12859-025-06146-9  

   Hsieh, Yin-Chen; Bockwoldt, Mathias; Heiland, Ines (December 2025, BMC Bioinformatics)

   Abstract Background:Protein presence information is an essential component of biological pathway identification. Presence of certain enzymes in an organism points towards the metabolic pathways that occur within it, whereas the absence of these enzymes indicates either the existence of alternative pathways or a lack of these pathways altogether. The same inference applies to regulatory pathways such as gene regulation and signal transduction. Protein presence information therefore forms the basis for biological pathway studies, and patterns in presence-absence across multiple organisms allow for comparative pathway analyses. Results:Here we present ProTaxoVis, a novel bioinformatic tool that extracts protein presence information from database queries and maps it to a taxonomic tree or heatmap. ProTaxoVis generates a large-scale overview of presence patterns in taxonomic clades of interest. This overview reveals protein distribution patterns, and this can be used to deduce pathway evolution or to probe other biological questions. ProTaxoVis combines and filters sequence query results to extract information on the distribution of proteins and translates this information into two types of visual outputs: taxonomic trees and heatmaps. The trees supplement their topology with scaled pie-chart representations per node of the presence of target proteins and combinations of these proteins, such that patterns in taxonomic groups can easily be identified. The heatmap visualisation shows presence and conservation of these proteins for a user-determined set of species, allowing for a more detailed view over a larger group of proteins as compared to the trees. ProTaxoVis also allows for visual quality checks of hits based on a coverage plot and a length histogram, which can be used to determine e-value and minimum protein length cutoffs. Tabular output of resulting data from the query, combined, and heatmap building step are saved and easily accessible for further analyses. Conclusions:We evaluate our tool with the phosphoribosyltransferases, a transferase enzyme family with notable distribution patterns amongst organisms of varying complexities and across Eukaryota, Bacteria, and Archaea. ProTaxoVis is open-source and available at:https://github.com/MolecularBioinformatics/ProTaxoVis. 

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3. Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids

   https://doi.org/10.1186/s12864-023-09529-5  

   Puri, Heena; Grover, Sajjan; Pingault, Lise; Sattler, Scott E.; Louis, Joe (December 2023, BMC Genomics)

   Abstract BackgroundThe sugarcane aphid (SCA;Melanaphis sacchari) has emerged as a key pest on sorghum in the United States that feeds from the phloem tissue, drains nutrients, and inflicts physical damage to plants. Previously, it has been shown that SCA reproduction was low and high on sorghum SC265 and SC1345 plants, respectively, compared to RTx430, an elite sorghum male parental line (reference line). In this study, we focused on identifying the defense-related genes that confer resistance to SCA at early and late time points in sorghum plants with varied levels of SCA resistance. ResultsWe used RNA-sequencing approach to identify the global transcriptomic responses to aphid infestation on RTx430, SC265, and SC1345 plants at early time points 6, 24, and 48 h post infestation (hpi) and after extended period of SCA feeding for 7 days. Aphid feeding on the SCA-resistant line upregulated the expression of 3827 and 2076 genes at early and late time points, respectively, which was relatively higher compared to RTx430 and SC1345 plants. Co-expression network analysis revealed that aphid infestation modulates sorghum defenses by regulating genes corresponding to phenylpropanoid metabolic pathways, secondary metabolic process, oxidoreductase activity, phytohormones, sugar metabolism and cell wall-related genes. There were 187 genes that were highly expressed during the early time of aphid infestation in the SCA-resistant line, including genes encoding leucine-rich repeat (LRR) proteins, ethylene response factors, cell wall-related, pathogenesis-related proteins, and disease resistance-responsive dirigent-like proteins. At 7 days post infestation (dpi), 173 genes had elevated expression levels in the SCA-resistant line and were involved in sucrose metabolism, callose formation, phospholipid metabolism, and proteinase inhibitors. ConclusionsIn summary, our results indicate that the SCA-resistant line is better adapted to activate early defense signaling mechanisms in response to SCA infestation because of the rapid activation of the defense mechanisms by regulating genes involved in monolignol biosynthesis pathway, oxidoreductase activity, biosynthesis of phytohormones, and cell wall composition. This study offers further insights to better understand sorghum defenses against aphid herbivory. 

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4. DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

   https://doi.org/10.1093/nar/gkad985  

   Basu, Sushmita; Zhao, Bi; Biró, Bálint; Faraggi, Eshel; Gsponer, Jörg; Hu, Gang; Kloczkowski, Andrzej; Malhis, Nawar; Mirdita, Milot; Söding, Johannes; et al (November 2023, Nucleic Acids Research)

   Abstract The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/. 

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5. Adaptive Remodeling of the Proteome in Pistachio Roots Under Salt Stress: Implications for Food and Energy Security in Arid Regions

   https://doi.org/10.1002/fes3.70151  

   Akbari, Mohammad; Singh, Rakesh K; Andriūnaitė, Elena; Reddy, Umesh; Farajpour, Mostafa; Simmons, Sanaa; Vishnudasan, Dalia; Charles, Sona; Suravajhala, Prashanth; Mahna, Nasser; et al (November 2025, Food and Energy Security)

   ABSTRACT Pistachio thrives in semi‐arid and arid environments and is highly adaptable to various abiotic stresses. However, soil salinization significantly threatens productivity, leading to considerable osmotic and ionic stress for these plants. Roots are the primary sites for stress perception and response; however, they remain understudied in woody crops, such asPistachio. This study examines the alterations in root protein expression and metabolic pathways in response to sodium chloride‐induced salt stress through biochemical and proteomic analyses. One‐year‐old pistachio rootstocks were treated with four different saline water regimes over a 100‐day period, and the total proteins were isolated from these samples. Over 1600 protein identifiers were detected, with comparative analysis revealing 245 proteins that were more abundant and 190 that were less abundant across three stress levels. Key pathways associated with stress tolerance, such as protein modification, folding, and heat shock protein (HSP) protection, were upregulated. An increase in secondary metabolites played a crucial role in detoxification. As salt stress intensified, the abundance of trafficking proteins increased, enhancing transporter activities. Active signaling pathways were observed at lower stress levels, while structural proteins became more critical at higher stress levels for maintaining cell membrane integrity. This cultivar exhibited enhanced kinase activities that regulate lipid and carbohydrate metabolism, thereby aiding in ion homeostasis and maintaining redox balance. The protein interaction network, mapped to orthologous proteins inArabidopsis thaliana, revealed clusters associated with cytosolic, carbohydrate, and amino acid metabolism contributing to salinity stress tolerance. The validation of proteomic data was performed by assessing corresponding changes in transcript levels. The study expands upon previous work by providing a comprehensive proteomic map of UCB‐1 pistachio rootstock across multiple salinity levels. The findings have practical implications for developing more resilient cultivars, supporting sustainable pistachio production in regions prone to salinity. 

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