Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.cas.cz/INTAA/) has established itself as a unique computational resource, which enables users to calculate the contribution of individual residues in a biomolecular structure to its total energy using a molecular mechanical scoring function. In this update, we describe major additions to the web server which help solidify its position as a robust, comprehensive resource for biomolecular structure analysis. Importantly, a new continuum solvation model was introduced, allowing more accurate representation of electrostatic interactions in aqueous media. In addition, a low-overhead pipeline for the estimation of evolutionary conservation in protein chains has been added. New visualization options were introduced as well, allowing users to easily switch between and interrelate the energetic and evolutionary views of the investigated structures.

• MeSH
• aminokyseliny chemie   MeSH
• internet MeSH
• konformace proteinů * MeSH
• molekulární modely MeSH
• proteiny chemie   MeSH
• software * MeSH
• statická elektřina MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• proteiny MeSH

Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/.

• Klíčová slova
• HGVS variant nomenclature, TP53 variants, database, variant annotation,
• MeSH
• anotace sekvence MeSH
• databáze genetické * MeSH
• genetická variace genetika   MeSH
• genomika trendy   MeSH
• internet MeSH
• lidé MeSH
• mutace MeSH
• nádorový supresorový protein p53 genetika   MeSH
• software * MeSH
• výpočetní biologie trendy   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nádorový supresorový protein p53 MeSH
• TP53 protein, human MeSH Prohlížeč

Biomacromolecular structural data make up a vital and crucial scientific resource that has grown not only in terms of its amount but also in its size and complexity. Furthermore, these data are accompanied by large and increasing amounts of experimental data. Additionally, the macromolecular data are enriched with value-added annotations describing their biological, physicochemical and structural properties. Today, the scientific community requires fast and fully interactive web visualization to exploit this complex structural information. This article provides a survey of the available cutting-edge web services that address this challenge. Specifically, it focuses on data-delivery problems, discusses the visualization of a single structure, including experimental data and annotations, and concludes with a focus on the results of molecular-dynamics simulations and the visualization of structural ensembles.

• Klíčová slova
• browser-based, data delivery, macromolecules, visualization, web-based,
• MeSH
• internet * MeSH
• makromolekulární látky chemie   MeSH
• počítačová grafika * MeSH
• software * MeSH
• uživatelské rozhraní počítače * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• makromolekulární látky MeSH

SUMMARY: We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (HSPs) in BLAST output to their plausible full length, and predicts their homology and secondary structures. The aim of the application is to aid to characterize subject RNAs in HSPs that come uncharacterized in BLAST output. The main advantages of the web-server are easy use and interactive analysis with search, filtering and data export options. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at rboanalyzer.elixir-czech.cz. The website frontend is implemented in Elm, while backend is implemented in Python and served by Apache.

• Publikační typ
• časopisecké články MeSH

The authors present an account on the historical development of the most important contemporary information network INTERNET from its beginnings in the sixties to the present time. They explain the historical circumstances of its development, elucidate its character and describe the creation and fusion of all main information networks during the seventies, eighties and nineties up to their present shape. They deal with the contemporary organizational structure of INTERNET, safety and reliability of transmitted information and values of its services. They explain terms like E-mail, Web, multimedia and discussion fora and describe how to join this gigantic information network in practice.

• MeSH
• dějiny 20. století MeSH
• internet * dějiny   organizace a řízení   MeSH
• lékařská informatika * MeSH
• počítačové komunikační sítě MeSH
• Check Tag
• dějiny 20. století MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• historické články MeSH
• Geografické názvy
• Spojené státy americké MeSH

BACKGROUND: Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations-e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible. RESULTS: In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. CONCLUSION: The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application ( https://acc2.ncbr.muni.cz ) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets.

• Klíčová slova
• Empirical methods, Parameterization, Partial atomic charges, Web service,
• Publikační typ
• časopisecké články MeSH

Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.

• Klíčová slova
• Aphanomyces astaci, Astacidae, Cambaridae, Endangered species, Invasive species, Open data, Parastacidae, Species distribution,
• MeSH
• Aphanomyces MeSH
• databáze faktografické MeSH
• ekosystém MeSH
• internet MeSH
• severní raci * mikrobiologie   MeSH
• sladká voda * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

• MeSH
• internet MeSH
• konformace proteinů MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely * MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• makromolekulární látky MeSH

Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.

• MeSH
• databáze proteinů * MeSH
• internet MeSH
• konformace proteinů MeSH
• lektiny chemie   MeSH
• makromolekulární látky chemie   MeSH
• molekulární konformace * MeSH
• molekulární modely MeSH
• software * MeSH
• vazebná místa MeSH
• zinkové prsty MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• LecB protein, Pseudomonas aeruginosa MeSH Prohlížeč
• lektiny MeSH
• makromolekulární látky MeSH

Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical properties influence the transport process. The tunnels are attractive hot spots for protein engineering and drug development. However, studying the ligand binding and unbinding using experimental techniques is challenging, while in silico methods come with their limitations, especially in the case of resource-demanding virtual screening pipelines. Caver Web 1.2 is a new version of the web server combining the capabilities for the detection of protein tunnels with the calculation of the ligand trajectories. The new version of the Caver Web server was expanded with the ability to fetch novel ligands from the Integrated Database of Small Molecules and with the fully automated virtual screening pipeline allowing for the fast evaluation of the predefined set of over 4,300 currently approved drugs. The virtual screening pipeline is accompanied by a comprehensive user interface, making it a viable service for the broader spectrum of companies and the academic user community. The web server is freely available for academic use at https://loschmidt.chemi.muni.cz/caverweb.

• Klíčová slova
• CIF, Crystallographic Information File, CSA, Catalytic Site Atlas, Caver, CaverDock, Channel, FDA, U.S. Food and Drug Administration, FDA-approved drug, IDSM, Integrated Database of Small Molecules, PDB, Protein Data Bank, Tunnel, Virtual screening, Web,
• Publikační typ
• časopisecké články MeSH