ELIXIR CZ Friday Coffee 2021 – SBC: an R package for simulation-based calibration and validation of statistical models and algorithms <span class="dashicons dashicons-calendar"></span>

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 SBC […]

ELIXIR CZ Friday Coffee 2021 – Approximation of collective variables by neural networks – Anncolvar <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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. 9. at 9:30 – SBC: […]

ELIXIR CZ Friday Coffee 2021 – OpenPonk: an Open Conceptual Modelling Platform <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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 at […]

ELIXIR CZ Friday Coffee 2021 – CaverDock: Analysis of Ligand Transport through Protein Tunnels <span class="dashicons dashicons-calendar"></span>

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 ligand […]

ELIXIR CZ Friday Coffee 2021 – IRESs, IRESite and HCVIVdb <span class="dashicons dashicons-calendar"></span>

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 a new […]

ELIXIR CZ Friday Coffee 2021 – EnzymeMiner & SoluProt: mining of soluble enzymes <span class="dashicons dashicons-calendar"></span>

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 NCBI […]

ELIXIR CZ Friday Coffee 2021 – cpPredictor: template based prediction of RNA <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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, but it also integrated within […]

ELIXIR CZ Friday Coffee 2021 – 2DProts: Family-wide 2D diagrams <span class="dashicons dashicons-calendar"></span>

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 structure elements. […]

ELIXIR CZ Friday Coffee 2021 – FireProt: Computational tool <span class="dashicons dashicons-calendar"></span>

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 is a novel […]

ELIXIR CZ Friday Coffee 2021 – SPCI of QSAR models <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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 – AmtDB – database of ancient human <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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 <span class="dashicons dashicons-calendar"></span>

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 additional […]

ELIXIR CZ Friday Coffee 2021 – Data Management with DSW <span class="dashicons dashicons-calendar"></span>

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 solution without […]

ELIXIR CZ Friday Coffee February 2021 <span class="dashicons dashicons-calendar"></span>

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 structures. Take a look at […]