Molecular visualization Dotaz Zobrazit nápovědu
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.
- 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
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.
elektronický časopis
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biologie
- oftalmologie
- histologie
- NLK Publikační typ
- elektronické časopisy
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/.
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.
SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.
- MeSH
- software * MeSH
- systémová biologie * MeSH
- Publikační typ
- časopisecké články MeSH
Using the QIAprep Spin Miniprep Kit -- and a Microcentrifuge 63 -- Contents -- Lab Session 8D Visualization -- Laboratory Exercise 68 -- Restriction Enzyme Analysis of Miniprep DNA 68 -- Lab Session 9B Visualization of Green Fluorescent Protein: Part 2 70 -- Introduction 70 -- Laboratory Exercise 70 -- Visualization
3rd ed. xxvi, 200 s. : il. ; 28 cm
- MeSH
- molekulární biologie MeSH
- proteinové inženýrství MeSH
- rekombinantní DNA MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- chemie, klinická chemie
- biologie
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.
Vaniloidy, aktivní složky některých pálivých rostlin, jakými jsou pálivá paprika a latex sukulentu Euphorbia resinifera, byly od nepaměti využívány k tišení bolestivých stavů. Přestože první písemné zmínky o využití vaniloidů se dochovaly již z počátku našeho letopočtu, dodnes přesně neznáme příčinu jejich analgetického účinku. Cílem tohoto příspěvku je informovat o současných poznatcích, které byly získaný o mechanizmech analgetického působení vaniloidů na buněčné a molekulární úrovni
Since time immemorial, people have used the effects of pungent vanilloid compounds such as resiniferatoxin and capsaicin for th e treatment of various painful disorders. Although the first written records on therapeutic use of vanilloids in pain treatment g o back thousands of years, the exact mechanisms of their analgesic action remain unclear. The aim of this summary is to provide a brie f overview of the current status of research on the antinociceptive effects of vanilloids at the cellular and molecular level.
- MeSH
- Capsicum fyziologie metabolismus účinky léků MeSH
- finanční podpora výzkumu jako téma MeSH
- financování organizované MeSH
- fosforylace fyziologie MeSH
- kapsaicin dějiny terapeutické užití MeSH
- kationtové kanály TRPV chemie terapeutické užití účinky léků MeSH
- lidé MeSH
- měření bolesti psychologie MeSH
- molekulární biologie metody MeSH
- neopioidní analgetika farmakokinetika farmakologie terapeutické užití MeSH
- práh bolesti fyziologie psychologie MeSH
- Check Tag
- lidé 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.
- MeSH
- elektronová kryomikroskopie * metody MeSH
- molekulární modely * MeSH
- software * MeSH
- viry chemie ultrastruktura MeSH
- Publikační typ
- časopisecké články MeSH
