ELIXIR CZ Friday Coffee 2021
We are sorry to inform you that due to ELIXIR CZ Annual Conference 2021 we need to skip a usual service introduction on Friday, 26 November. Join us for the conference, registration is open until 11 November, or have a look on our video library on YouTube. We look forward to meeting you online at […]
ELIXIR CZ Friday Coffee 2021 – CalFitter: a web server for analysis of protein thermal denaturation data
Speaker: Stanislav Mazurenko from International Clinical Research Center of the St. Anne’s University Hospital in Brno Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a […]
ELIXIR CZ Friday Coffee 2021 – Decryptor: a tool for detecting variant peptides using mass spectrometry
Speaker: Miroslav Hruška from Palacký University Olomouc Decryptor is an online service that allows detecting human variant peptides in typical shotgun proteomics data. The system searches mass spectra against a database of peptide variants constructed from nucleotide variants observed globally on DNA or mRNA level. Detection of variant peptides allows researchers to focus on sequence-specific […]
ELIXIR CZ Friday Coffee 2021
Due to unexpected circumstances the Friday coffee today is canceled. We are sorry for any inconvenience. Registration is not needed. Join the webinar in GoToMeeting» We value your opinion. Please give us your feedback on the webinar» Future webinars 12. 11. at 9:30 – Decryptor: a tool for detecting variant peptides using mass spectrometry.19. 11. at 9:30 – […]
ELIXIR CZ Friday Coffee 2021 – MOLE: Analysis of Protein Channels
Speaker: Karel Berka from Palacký University Olomouc MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. The tool is interconnected with […]
ELIXIR CZ Friday Coffee 2021 – WebMMB
Speaker: Michal Malý from Institute of Biotechnology of the Czech Academy of Sciences The newly developed web interface for the MMB (MacroMoleculeBuilder) program will be presented. It concentrates on user-friendly building of initial models and modification of existing nucleic acid structures.Registration is not needed. Join the webinar in GoToMeeting» We value your opinion. Please give […]
ELIXIR CZ Friday Coffee 2021 – ACC II: Calculation of partial atomic charges
Speaker: Radka Svobodová from Masaryk University Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast […]
ELIXIR CZ Friday Coffee 2021 – RepeatExplorer Galaxy Server: Tools for Genome Assembly Annotation
Speaker: Petr Novák from Biology Centre of the Czech Academy of Sciences RepeatExplorer Galaxy Server provides several tools for discovering and annotation of repetitive elements. Most notably, these include tools such as RepeatExplorer2 or TAREAN pipelines, which can be used to characterize repetitive sequences directly from unassembled sequence reads. Several other tools on the RE […]
ELIXIR CZ Friday Coffee 2021 – ASAFind 2.0: Multi-class predictions of intracellular locations of proteins in organisms with complex plastids
Speaker: Ansgar Gruber from University of South Bohemia in České Budějovice and Biology Centre of the CAS Plastids of diatoms and related algae with complex plastids of red algal origin, are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as […]
ELIXIR CZ Friday Coffee 2021 – SBC: an R package for simulation-based calibration and validation of statistical models and algorithms
Speaker: Martin Modrák from the Institute of Microbiology of the Czech Academy of Sciences Simulation studies are an important part of validation for any statistical tool. In the context of Bayesian models, there are consistency results that can be used to check that the implementation of a model or an inference algorithm is correct. The […]
ELIXIR CZ Friday Coffee 2021 – Approximation of collective variables by neural networks – Anncolvar
Approximation of collective variables by neural networks – Anncolvar Vojtech Spiwok from UCT Many methods have been developed to accelerate molecular dynamics simulations. Some of these methods are based on artificial forces applied on certain descriptors of the molecular systems, also known as collective variables. Some potentially useful collective variables are impossible or difficult to […]
ELIXIR CZ Friday Coffee 2021 – PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships Martin Kolisko, Matthew W Brown from BC, JU Meet us online every friday morning to explore the portfolio of ELIXIR CZ tools and services at https://global.gotomeeting.com/join/508817845 . Registration is not needed Future webinars 17. 9. at 9:30 – Approximation of collective variables by neural networks – Anncolvar.24. […]
ELIXIR CZ Friday Coffee 2021 – OpenPonk: an Open Conceptual Modelling Platform
OpenPonk: an Open Conceptual Modelling Platform Robert Pergl, Jan Blizničenko from CTU OpenPonk is an open platform for conceptual modelling. It offers several notations for structural and behavioural modelling, but most importantly, it is open for extending by new notations, visualisations, simulations, algorithms and integrations. During the session, we introduce the platform and its basic […]
ELIXIR CZ Friday Coffee 2021 – PrankWeb
PrankWeb Marian Novotný from UK PrankWeb (https://prankweb.cz/) is a tool predicting ligand binding sites on 3D structures using machine learning algorithms. The tool is integrated into the PDBe-KB. We will present both its current state and its future developments. Meet us online every friday morning to explore the portfolio of ELIXIR CZ tools and services […]
ELIXIR CZ Friday Coffee 2021 – CaverDock: Analysis of Ligand Transport through Protein Tunnels
CaverDock: Analysis of Ligand Transport through Protein Tunnels Ondřej Vávra from ICRC Understanding protein-ligand interactions is crucial for drug design and enzyme engineering. The interaction of protein and small ligand molecule often takes place in protein’s binding or active site. Such functional sites may be buried inside the protein core, and thus transport of a […]
ELIXIR CZ Friday Coffee 2021 – IRESs, IRESite and HCVIVdb
IRESs, IRESite and HCVIVdb Martin Pospíšek from PřF UK Our long-term interest in internal ribosome entry sites (IRES) resulted in development of two specialized databases – IRESite presenting information about the known experimentally studied IRESs, their structures and supporting experiments, and HCVIVdb, which is specialised in variants of the hepatitis C virus IRES. We’ll also present […]
ELIXIR CZ Friday Coffee 2021 – EnzymeMiner & SoluProt: mining of soluble enzymes
EnzymeMiner & SoluProt: mining of soluble enzymes Jiří Hon from ICRC We present two integrated bioinformatics tools EnzymeMiner and SoluProt for mining and rational selection of novel soluble enzymes. EnzymeMiner uses one or more enzyme sequences and a description of essential residues to find enzyme family members among millions of uncharacterized protein sequences in the […]
ELIXIR CZ Friday Coffee 2021 – cpPredictor: template based prediction of RNA
cpPredictor: template based prediction of RNA secondary structures Josef Pánek from MBU Cpredict is an algorithm for template-based prediction of secondary structures of RNAs. As templates, experimentally identified RNA structures are used. Reliability of predicted structures is evaluated by bootstrapping. Meet us online every friday morning to explore the portfolio of ELIXIR CZ tools and services at […]
ELIXIR CZ Friday Coffee 2021 – Traveler: visualization of secondary structure of RNA
Traveler: visualization of secondary structure of RNA molecules David Hoksza from UK Traveler is a tool for template-based visualization of RNA secondary structure. If a sufficiently close template is available, Traveler is able to generate a layout for even the largest RNA molecules in a standard orientation. Traveler can be used as a stand-alone application, […]
ELIXIR CZ Friday Coffee 2021 – 2DProts: Family-wide 2D diagrams
2DProts: Family-wide 2D diagrams of protein secondary structure Radka Svobodová from MU 2DProts database contains secondary structure 2D diagrams for proteins and protein domains. Moreover, it includes multiple 2D diagrams of protein family’s secondary structures. The 2D diagrams are generated based on a whole protein family, and consider information about the 3D arrangement of secondary […]
ELIXIR CZ Friday Coffee 2021 – FireProt: Computational tool
FireProt: Computational tool for the design of stable proteins Miloš Musil from ICRC FireProt is a family of tools for the design and analysis of stable proteins. FireProt-web is a server for the fully automated design of stable multiple-point mutants, while FireProt-ASR helps inexperienced users with the successful utilization of ancestral sequence reconstruction. Finally, FireProt-DB […]
ELIXIR CZ Friday Coffee 2021 – SPCI of QSAR models
SPCI: Structural and physicochemical interpretation of QSAR models Pavel Polishchuk from UPOL The SPCI tool enables automatic building of quantitative structure-activity relationship (QSAR) models and their interpretation. Interpretation is performed in terms of contribution of individual atoms or substructures into the modeling activity which information can be used for molecule optimization and visualization of structure-activity relationship […]
ELIXIR CZ Friday Coffee 2021 – Metadynminer and Metadynreporter
Metadynminer and Metadynreporter Vojtěch Spiwok from UCT Biomolecular simulations are computationally expensive calculations. For this reason most simulations nowadays span nanosecond or microsecond time scales. Many interesting processes, such as protein-ligand binding or protein-folding take place in much longer time scales. Metadynamics is one of most popular method developed to accelerate molecular simulations. We have […]
ELIXIR CZ Friday Coffee 2021 – ELIXIR and Galaxy Project
ELIXIR and Galaxy Project Martin Čech from IOCB Galaxy is a tool that assists scientists with making their software pipelines reproducible, portable, and easy to share. This session presents a 10,000 feet overview of the Galaxy Project – what it is, what it does and how to start using it. We’ll also cover communities like […]
ELIXIR CZ Friday Coffee 2021 – AmtDB – database of ancient human
AmtDB – database of ancient human full mitogenomes and sample metadata Edvard Ehler from IMG Our AmtDB (https://amtdb.org/) represents today the most complete open online source of aDNA samples (mitogenomes) and additional information about the samples, their archaeological context, dating, location and publication. In last two years, we have updated our database significantly, adding new […]
ELIXIR CZ Friday Coffee 2021 – Nucleic Acid Conformations
Nucleic Acid Conformations (dnatco.datmos.org) Jiří Černý from BTU A detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids will be presented. The web server performs an assignment of the nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids. Meet us […]
ELIXIR CZ Friday Coffee 2021 – Mol* visualization of biomacromolecules
Mol* visualization of biomacromolecules David Sehnal from MU The Mol* Viewer (https://molstar.org/) enables 3D visualisation of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. Mol* Viewer also allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, […]
ELIXIR CZ Friday Coffee 2021 – GlobalFungi database
GlobalFungi database – global fungal community composition obtained by NGS Tomáš Větrovský from MBU The GlobalFungi database represents the world most comprehensive atlas of global fungal distribution based on the fungal internal transcribed spacers. The current version of the database contains almost 800 million observations of fungal sequences across 27 000 samples with geographical locations and […]
ELIXIR CZ Friday Coffee 2021 – Data Management with DSW
Data Management with Data Stewardship Wizard Tereza Machačová and Jana Freeman from CTU FIT The presentation briefly introduces students to data management planning and the possibility of creating data management plans for their projects using Data Stewardship Wizard. This tool serves as a smart guide to this complex problematics and offers a simple and effective […]
ELIXIR CZ Friday Coffee February 2021
Meet us online every Friday morning to explore the portfolio of ELIXIR CZ tools and services. February 5.2. at 9:30Jakyb Galgonek from IOCBIDSM : Integrated Database of Small Molecules.Take a look at the webinar and give us your feedback. 12.2. at 9:30Dávid Jakubec from IOCBINTAA and 3DPatch : exploration of energetics and conservation in biomolecular 3D […]
