Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from a given three-dimensional structure. It provides access to P2Rank, a state-of-the-art machine learning tool for binding site prediction. Here, we present a new version of PrankWeb enabling the development of both client- and server-side modules acting as postprocessing tasks on the predicted pockets. Furthermore, each module can be associated with a visualization module that acts on the results provided by both client- and server-side modules. This newly developed system was utilized to implement the ability to dock user-provided molecules into the predicted pockets using AutoDock Vina (server-side module) and to interactively visualize the predicted poses (visualization module). In addition to introducing a modular architecture, we revamped PrankWeb's interface to better support the modules and enhance user interaction between the 1D and 3D viewers. We introduced a new, faster P2Rank backend or user-friendly exports, including ChimeraX visualization.

• MeSH
• Internet MeSH
• Protein Conformation MeSH
• Ligands MeSH
• Proteins * chemistry   metabolism   MeSH
• Molecular Docking Simulation MeSH
• Software * MeSH
• Machine Learning MeSH
• User-Computer Interface MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Ligands MeSH
• Proteins * MeSH

The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has no login requirement.

• MeSH
• Databases, Protein * MeSH
• Internet MeSH
• Protein Conformation MeSH
• Quantum Theory MeSH
• Proteins * chemistry   MeSH
• Software * MeSH
• Static Electricity MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Proteins * MeSH

Enzymes with buried active sites utilize molecular tunnels to exchange substrates, products, and solvent molecules with the surface. These transport mechanisms are crucial for protein function and influence various properties. As proteins are inherently dynamic, their tunnels also vary structurally. Understanding these dynamics is essential for elucidating structure-function relationships, drug discovery, and bioengineering. Caver Web 2.0 is a user-friendly web server that retains all Caver Web 1.0 functionalities while introducing key improvements: (i) generation of dynamic ensembles via automated molecular dynamics with YASARA, (ii) analysis of dynamic tunnels with CAVER 3.0, (iii) prediction of ligand trajectories in multiple snapshots with CaverDock 1.2, and (iv) customizable ligand libraries for virtual screening. Users can assess protein flexibility, identify and characterize tunnels, and predict ligand trajectories and energy profiles in both static and dynamic structures. Additionally, the platform supports virtual screening with FDA/EMA-approved drugs and user-defined datasets. Caver Web 2.0 is a versatile tool for biological research, protein engineering, and drug discovery, aiding the identification of strong inhibitors or new substrates to bind to the active sites or tunnels, and supporting drug repurposing efforts. The server is freely accessible at https://loschmidt.chemi.muni.cz/caverweb.

• MeSH
• Internet MeSH
• Catalytic Domain MeSH
• Protein Conformation MeSH
• Ligands MeSH
• Drug Discovery MeSH
• Proteins * chemistry   metabolism   MeSH
• Molecular Dynamics Simulation MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Ligands MeSH
• Proteins * MeSH

Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

• MeSH
• Internet MeSH
• Computer Graphics * MeSH
• Software * MeSH
• User-Computer Interface MeSH
• Publication type
• Journal Article MeSH

BACKGROUND: Defects of mitochondrial ATP synthase (ATPase) represent an emerging, yet incompletely understood group of neurodevelopmental diseases with abnormal movements. OBJECTIVE: The aim of this study was to redefine the phenotypic and mutational spectrum of movement disorders linked to the ATPase subunit-encoding genes ATP5F1A and ATP5F1B. METHODS: We recruited regionally distant patients who had been genome or exome sequenced. Fibroblast cultures from two patients were established to perform RNA sequencing, immunoblotting, mass spectrometry-based high-throughput quantitative proteomics, and ATPase activity assays. In silico three-dimensional missense variant modeling was performed. RESULTS: We identified a patient with developmental delay, myoclonic dystonia, and spasticity who carried a heterozygous frameshift c.1404del (p.Glu469Serfs*3) variant in ATP5F1A. The patient's cells exhibited significant reductions in ATP5F1A mRNA, underexpression of the α-subunit of ATPase in association with other aberrantly expressed ATPase components, and compromised ATPase activity. In addition, a novel deleterious heterozygous ATP5F1A missense c.1252G>A (p.Gly418Arg) variant was discovered, shared by three patients from two families with hereditary spastic paraplegia (HSP). This variant mapped to a functionally important intersubunit communication site. A third heterozygous variant, c.1074+1G>T, affected a canonical donor splice site of ATP5F1B and resulted in exon skipping with significantly diminished ATP5F1B mRNA levels, as well as impaired ATPase activity. The associated phenotype consisted of cerebral palsy (CP) with prominent generalized dystonia. CONCLUSIONS: Our data confirm and expand the role of dominant ATP5F1A and ATP5F1B variants in neurodevelopmental movement disorders. ATP5F1A/ATP5F1B-related ATPase diseases should be considered as a cause of dystonia, HSP, and CP. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

• Keywords
• ATP synthase, ATP5F1A, ATP5F1B, cerebral palsy, dominant variant, dystonia, mitochondrial disease, spasticity,
• MeSH
• Alleles MeSH
• Child MeSH
• Phenotype MeSH
• Humans MeSH
• Mitochondrial Proton-Translocating ATPases * genetics   MeSH
• Mutation genetics   MeSH
• Movement Disorders * genetics   MeSH
• Check Tag
• Child MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH
• Names of Substances
• ATP5F1A protein, human MeSH Browser
• ATP5F1B protein, human MeSH Browser
• Mitochondrial Proton-Translocating ATPases * MeSH

Plasmodiophora brassicae is one of the most devastating threats to Brassicaceae crops. However, the molecular mechanisms underlying clubroot disease remain unclear. Initial proteomics results led us to hypothesize that HSP70 proteins regulate host-P. brassicae interactions by modulating both plant defenses and pathogen activity. Using the Arabidopsis thaliana-P. brassicae model system, we studied the role of HSP70 proteins in detail. Through a combination of proteomics and mutant phenotype analyses, we indicate that Plasmodiophora infection induces HSP70 accumulation in Arabidopsis roots, and mutations in specific HSP70 isoforms either promote (HSP70-1, HSP70-13, HSP70-14) or suppress (HSP70-5, HSP70-12) the onset of clubroot disease. Proteomic profiling of root galls showed strong correlations between infection severity and pathogen-derived HSP70 protein CEO96729. Interactomics analyses revealed that CEO96729 interacts with host proteins involved in plant response to Plasmodiophora infection, including an extracellular GDSL esterase/lipase with a putative role in long-distance signaling, and that CEO96729 forms heterodimers with host HSP70 isoforms. These findings suggest that Plasmodiophora hijacks the host chaperone machinery to facilitate infection, offering a potential explanation for the observed modulation of disease progression in HSP70 mutants. Notably, the results also point to possible intracellular interactions with key enzymes in host physiology, including catalase 2, essential for ROS metabolism, and nitrilase, critical for auxin biosynthesis and root gall formation. Collectively, our study highlights the multifaceted roles of HSP70 proteins in Plasmodiophora pathogenicity and host-pathogen interactions, providing insights into chaperone-mediated processes in plant immunity and infection dynamics.

• Keywords
• clubroot disease, interactomics, plant immunity, plant‐pathogen interaction, proteomics,
• MeSH
• Arabidopsis * parasitology   genetics   metabolism   MeSH
• Host-Pathogen Interactions * physiology   MeSH
• Plant Roots parasitology   metabolism   genetics   MeSH
• Mutation MeSH
• Plant Diseases * parasitology   immunology   MeSH
• Plasmodiophorida * physiology   MeSH
• Arabidopsis Proteins * metabolism   genetics   MeSH
• HSP70 Heat-Shock Proteins * metabolism   genetics   MeSH
• Proteomics MeSH
• Gene Expression Regulation, Plant MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Arabidopsis Proteins * MeSH
• HSP70 Heat-Shock Proteins * MeSH

The carbohydrate 3D structure-prediction tools (builders) at GLYCAM-Web (glycam.org) are widely used for generating experimentally-consistent 3D structures of oligosaccharides suitable for data interpretation, hypothesis generation, simple visualization, and subsequent molecular dynamics (MD) simulation. The graphical user interface (GUI) enables users to create carbohydrate sequences (e.g. DGalpb1-4DGlcpb1-OH) that are converted to 3D models of the carbohydrate structures in multiple formats, including PDB and OFF (AMBER software format). The resulting structures are energy minimized prior to download and online visualization. There are advanced options for selecting which shapes (rotamers) of the oligosaccharide to generate, and for creating explicitly solvated structures for subsequent MD simulation. The GLYCAM-Web builders integrate known conformational preferences of oligosaccharides, summarized here, and employ the GLYCAM forcefield for energy minimization with algorithms tailored for speed and scalability. Even for large oligosaccharides (100 residues, ~2100 atoms) a 3D structure is typically returned to the user in less than a minute.

• Publication type
• Journal Article MeSH
• Preprint MeSH

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools-allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

• Keywords
• 3D biostructure, Protein Data Bank, global health, influenza A H5N1 virus, molecular visualization, open‐source, pandemic preparedness, viral pathogen, virus life cycle, web‐based,
• MeSH
• Databases, Protein MeSH
• Internet MeSH
• Protein Conformation MeSH
• Models, Molecular MeSH
• Proteome * chemistry   MeSH
• Software * MeSH
• Viral Proteins * chemistry   MeSH
• Influenza A Virus, H5N1 Subtype * chemistry   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Proteome * MeSH
• Viral Proteins * MeSH

Heme is essential for all organisms. The composition and location of the pathway for heme biosynthesis, have been influenced by past endosymbiotic events and organelle evolution in eukaryotes. Endosymbioses led to temporary redundancy of the enzymes and the genes involved. Genes were transferred to the nucleus from different endosymbiotic partners, and their multiple copies were either lost or retained, resulting in a mosaic pathway. This mosaic is particularly complex in organisms with eukaryote-derived plastids, such as diatoms. The plastids of diatoms are clearly derived from red algae. However, it is not entirely clear whether they were acquired directly from a red algal ancestor or indirectly in higher-order endosymbioses. In the diatom Phaeodactylum tricornutum, most enzymes of the pathway are present in a single copy, but three, glutamyl-tRNA synthetase (GluRS), uroporphyrinogen decarboxylase (UROD) and coproporphyrinogen oxidase (CPOX), are encoded in multiple copies. These are not direct paralogs resulting from gene duplication within the lineage but were acquired horizontally during the plastid endosymbioses. While some iso-enzymes originate from the host cell, others originate either from the genome of the cyanobacterial ancestor of all plastids or from the nuclear genome of the eukaryotic ancestor of the diatom complex plastid, a rhodophyte or an alga containing rhodophyte-derived plastids, a situation known as pseudoparalogy. Using green fluorescent protein-tagged expression and immunogold labeling, we experimentally localized all enzymes of the pathway in P. tricornutum, and confirmed their localization in the plastid, with a few possible exceptions. Our meta-analyses of transcription data showed that the pseudoparalogs are differentially expressed in response to nitrate starvation, blue light, high light, high CO2, and the cell cycle. Taken together, our findings emphasize that the evolution of complex plastids via endosymbiosis has a direct impact not only on the genetics but also on the physiology of resulting organisms.

• Keywords
• algae, chloroplast, endosymbiosis, evolution, horizontal gene transfer, organelle, tetrapyrrole,
• Publication type
• Journal Article MeSH

RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.

• MeSH
• Polymorphism, Single Nucleotide MeSH
• Nucleic Acid Conformation * MeSH
• Computer Graphics MeSH
• RNA * chemistry   genetics   MeSH
• RNA Folding MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• RNA * MeSH