Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/.

• MeSH
• internet * MeSH
• konformace proteinů MeSH
• proteiny * chemie   ultrastruktura   MeSH
• virtuální realita * MeSH
• výpočetní biologie metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• proteiny * 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.

• Klíčová slova
• 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
• databáze proteinů MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• proteom * chemie   MeSH
• software * MeSH
• virové proteiny chemie   MeSH
• virus chřipky A, podtyp H5N1 * chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteom * MeSH
• virové proteiny MeSH

This paper focuses on the method for creating 3-dimensional (3D) digital models extracted from patient- specific scans of the brain. The described approach consists of several cross-platform stages: raw data segmentation, data correction in 3D-modelling software, post-processing of the 3D digital models and their presentation on an interactive web-based platform. This method of data presentation offers a cost and time effective option to present medical data accurately. An important aspect of the process is using real patient data and enriching the traditional slice-based representation of the scans with 3D models that can provide better understanding of the organs' structures. The resulting 3D digital models also form the basis for further processing into different modalities, for example models in Virtual Reality or 3D physical model printouts. The option to make medical data less abstract and more understandable can extend their use beyond diagnosis and into a potential aid in anatomy and patient education. The methods presented in this paper were originally based on the master thesis 'Transparent Minds: Testing for Efficiency of Transparency in 3D Physical and 3D Digital Models', which focussed on creating and comparing the efficiency of transparent 3D physical and 3D digital models from real-patient data.

• Klíčová slova
• 3D models, Alzheimer’s disease, data segmentation, medical art, medical visualization, patient data,
• MeSH
• anatomické modely * MeSH
• lidé MeSH
• mozek MeSH
• software MeSH
• virtuální realita * MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The advent of cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), coupled with computational modeling, has enabled the creation of integrative 3D models of viruses, bacteria, and cellular organelles. These models, composed of thousands of macromolecules and billions of atoms, have historically posed significant challenges for manipulation and visualization without specialized molecular graphics tools and hardware. With the recent advancements in GPU rendering power and web browser capabilities, it is now feasible to render interactively large molecular scenes directly on the web. In this work, we introduce Mesoscale Explorer, a web application built using the Mol* framework, dedicated to the visualization of large-scale molecular models ranging from viruses to cell organelles. Mesoscale Explorer provides unprecedented access and insight into the molecular fabric of life, enhancing perception, streamlining exploration, and simplifying visualization of diverse data types, showcasing the intricate details of these models with unparalleled clarity.

• Klíčová slova
• 3D animation, interactive tours, mesoscale models, molecular graphism, web-based 3D visualization,
• Publikační typ
• časopisecké články MeSH
• preprinty MeSH

The advent of cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), coupled with computational modeling, has enabled the creation of integrative 3D models of viruses, bacteria, and cellular organelles. These models, composed of thousands of macromolecules and billions of atoms, have historically posed significant challenges for manipulation and visualization without specialized molecular graphics tools and hardware. With the recent advancements in GPU rendering power and web browser capabilities, it is now feasible to render interactively large molecular scenes directly on the web. In this work, we introduce Mesoscale Explorer, a web application built using the Mol* framework, dedicated to the visualization of large-scale molecular models ranging from viruses to cell organelles. Mesoscale Explorer provides unprecedented access and insight into the molecular fabric of life, enhancing perception, streamlining exploration, and simplifying visualization of diverse data types, showcasing the intricate details of these models with unparalleled clarity.

• Klíčová slova
• 3D animation, interactive tours, mesoscale models, molecular graphism, web‐based 3D visualization,
• MeSH
• elektronová kryomikroskopie * metody   MeSH
• molekulární modely * MeSH
• software * MeSH
• viry chemie   ultrastruktura   MeSH
• Publikační typ
• časopisecké články MeSH

Ever-increasing availability of experimental volumetric data (e.g., in .ccp4, .mrc, .map, .rec, .zarr, .ome.tif formats) and advances in segmentation software (e.g., Amira, Segger, IMOD) and formats (e.g., .am, .seg, .mod, etc.) have led to a demand for efficient web-based visualization tools. Despite this, current solutions remain scarce, hindering data interpretation and dissemination. Previously, we introduced Mol* Volumes & Segmentations (Mol* VS), a web application for the visualization of volumetric, segmentation, and annotation data (e.g., semantically relevant information on biological entities corresponding to individual segmentations such as Gene Ontology terms or PDB IDs). However, this lacked important features such as the ability to edit annotations (e.g., assigning user-defined descriptions of a segment) and seamlessly share visualizations. Additionally, setting up Mol* VS required a substantial programming background. This article presents an updated version, Mol* VS 2.0, that addresses these limitations. As part of Mol* VS 2.0, we introduce the Annotation Editor, a user-friendly graphical interface for editing annotations, and the Volumes & Segmentations Toolkit (VSToolkit) for generating shareable files with visualization data. The outlined protocols illustrate the utilization of Mol* VS 2.0 for visualization of volumetric and segmentation data across various scales, showcasing the progress in the field of molecular complex visualization. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: VSToolkit-setting up and visualizing a user-constructed Mol* VS 2.0 database entry Basic Protocol 2: VSToolkit-visualizing multiple time frames and volume channels Support Protocol 1: Example: Adding database entry idr-13457537 Alternate Protocol 1: Local-server-and-viewer-visualizing multiple time frames and volume channels Support Protocol 2: Addition of database entry custom-tubhiswt Basic Protocol 3: VSToolkit-visualizing a specific channel and time frame Basic Protocol 4: VSToolkit-visualizing geometric segmentation Basic Protocol 5: VSToolkit-visualizing lattice segmentations Alternate Protocol 2: "Local-server-and-viewer"-visualizing lattice segmentations Basic Protocol 6: "Local-server-and-viewer"-visualizing multiple volume channels Support Protocol 3: Deploying a server API Support Protocol 4: Hosting Mol* viewer with VS extension 2.0 Support Protocol 5: Example: Addition of database entry empiar-11756 Support Protocol 6: Example: Addition of database entry emd-1273 Support Protocol 7: Editing annotations Support Protocol 8: Addition of database entry idr-5025553.

• Klíčová slova
• 3D visualization tools, annotation data, large‐scale datasets, segmentation data, volumetric data,
• MeSH
• internet MeSH
• počítačová grafika MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• vizualizace dat MeSH
• Publikační typ
• časopisecké články MeSH

Segmentation helps interpret imaging data in a biological context. With the development of powerful tools for automated segmentation, public repositories for imaging data have added support for sharing and visualizing segmentations, creating the need for interactive web-based visualization of 3D volume segmentations. To address the ongoing challenge of integrating and visualizing multimodal data, we developed Mol* Volumes and Segmentations (Mol*VS), which enables the interactive, web-based visualization of cellular imaging data supported by macromolecular data and biological annotations. Mol*VS is fully integrated into Mol* Viewer, which is already used for visualization by several public repositories. All EMDB and EMPIAR entries with segmentation datasets are accessible via Mol*VS, which supports the visualization of data from a wide range of electron and light microscopy experiments. Additionally, users can run a local instance of Mol*VS to visualize and share custom datasets in generic or application-specific formats including volumes in .ccp4, .mrc, and .map, and segmentations in EMDB-SFF .hff, Amira .am, iMod .mod, and Segger .seg. Mol*VS is open source and freely available at https://molstarvolseg.ncbr.muni.cz/.

• MeSH
• internet MeSH
• makromolekulární látky MeSH
• mikroskopie * MeSH
• počítačové zpracování obrazu * MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• makromolekulární látky MeSH

AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.

• MeSH
• databáze proteinů * MeSH
• internet MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• proteom * chemie   genetika   MeSH
• sbalování proteinů MeSH
• software * MeSH
• strojové učení MeSH
• strukturní homologie proteinů MeSH
• vyhledávač MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny MeSH
• proteom * MeSH

BACKGROUND: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. RESULTS: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. CONCLUSION: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

• MeSH
• algoritmy * MeSH
• internet * MeSH
• konformace nukleové kyseliny * MeSH
• RNA chemie   MeSH
• sekvenční analýza RNA metody   MeSH
• sekvenční seřazení metody   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• RNA MeSH

SUMMARY: Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. AVAILABILITY AND IMPLEMENTATION: Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• databáze faktografické MeSH
• proteiny * chemie   MeSH
• sekundární struktura proteinů MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny * MeSH