We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.

• Klíčová slova
• DNA nanotechnology, modelitics, molecular dynamics, molecular visualization, visual abstraction,
• MeSH
• Bacteria MeSH
• DNA ultrastruktura   MeSH
• lidé MeSH
• molekulární modely MeSH
• nanostruktury * MeSH
• proteiny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• DNA MeSH
• proteiny MeSH

BACKGROUND: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. RESULTS: We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations. By introducing the information about mutual positions of protein chains into the 1D sequential representation the users are able to observe the spatial differences between the proteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely for comparison of multiple proteins or a set of time steps of molecular dynamics simulation. CONCLUSIONS: The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare a set of proteins from the family of cytochromes P450 where the position of the secondary structures has a significant impact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a set of time steps our representation helps to reveal the most dynamically changing parts of the protein chain.

• Klíčová slova
• Molecular sequence analysis, Molecular structure and function, Molecular visualization,
• MeSH
• algoritmy MeSH
• molekulární modely MeSH
• proteiny chemie   MeSH
• sekundární struktura proteinů * MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny MeSH

SUMMARY: MolArt fills the gap between sequence and structure visualization by providing a light-weight, interactive environment enabling exploration of sequence annotations in the context of available experimental or predicted protein structures. Provided a UniProt ID, MolArt downloads and displays sequence annotations, sequence-structure mapping and relevant structures. The sequence and structure views are interlinked, enabling sequence annotations being color overlaid over the mapped structures, thus providing an enhanced understanding and interpretation of the available molecular data. AVAILABILITY AND IMPLEMENTATION: MolArt is released under the Apache 2 license and is available at https://github.com/davidhoksza/MolArt. The project web page https://davidhoksza.github.io/MolArt/ features examples and applications of the tool.

• MeSH
• barva MeSH
• konformace proteinů * MeSH
• molekulární struktura * MeSH
• proteiny * MeSH
• software * MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny * MeSH

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 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

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

With the ever-expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: https://molstar.org/mol-view-spec/, GitHub project: https://github.com/molstar/mol-view-spec), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view-building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball-and-stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python package Basic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation files Basic Protocol 3: Creating a MolViewSpec view with labels and other advanced features Support Protocol 1: Computing rotation and translation vectors Support Protocol 2: Creating a MolViewSpec annotation file.

• Klíčová slova
• 3D visualization, Protein Data Bank, interoperability, macromolecular structure, mmCIF,
• MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• software * MeSH
• zobrazování trojrozměrné MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• makromolekulární látky MeSH

MOTIVATION: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. RESULTS: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. AVAILABILITY AND IMPLEMENTATION: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• algoritmy MeSH
• konformace proteinů MeSH
• proteinové inženýrství MeSH
• proteiny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny MeSH

The design of metal-organic interfaces with atomic precision enables the fabrication of highly efficient devices with tailored functionality. The possibility of fast and reliable analysis of molecular stacking order at the interface is of crucial importance, as the interfacial stacking order of molecules directly influences the quality and functionality of fabricated organic-based devices. Dark-field (DF) imaging using Low-Energy Electron Microscopy (LEEM) allows the visualization of areas with a specific structure or symmetry. However, distinguishing layers with different stacking orders featuring the same diffraction patterns becomes more complicated. Here we show that the top layer shift in organic molecular bilayers induces measurable differences in spot intensities of respective diffraction patterns that can be visualized in DF images. Scanning Tunneling Microscopy (STM) imaging of molecular bilayers allowed us to measure the shift directly and compare it with the diffraction data. We also provide a conceptual diffraction model based on the electron path differences, which qualitatively explains the observed phenomenon.

• Klíčová slova
• Dark-field contrast, Layer stacking, Low-energy electron microscopy, Self-assembly,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Visualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern methods of high-throughput screening generate large amounts of molecular data that call for methods enabling their analysis. One such method is classification of compounds based on their molecular scaffolds, a concept widely used by medicinal chemists to group molecules of similar properties. This classification can then be utilized for intuitive visualization of compounds. RESULTS: In this paper, we propose a scaffold hierarchy as a result of large-scale analysis of the PubChem Compound database. The analysis not only provided insights into scaffold diversity of the PubChem Compound database, but also enables scaffold-based hierarchical visualization of user compound data sets on the background of empirical chemical space, as defined by the PubChem data, or on the background of any other user-defined data set. The visualization is performed by a web based client-server application called Scaffvis. It provides an interactive zoomable tree map visualization of data sets up to hundreds of thousands molecules. Scaffvis is free to use and its source codes have been published under an open source license.Graphical abstract.

• Klíčová slova
• Chemical space, Pubchem, Scaffold, Treemap, Visualization,
• Publikační typ
• časopisecké články MeSH