ELIXIR CZ Friday Coffee 2021
Every Friday ELIXIR CZ organizes webinars to explore their portfolio of tools and services. Registration is not needed: https://global.gotomeeting.com/join/508817845
Recordings are published at ELIXIR CZ YouTube channel.
June
4.6.: EnzymeMiner & SoluProt: mining of soluble enzymes
11.6.: IRESs, IRESite and HCVIVdb
18.6.: CaverDock: Analysis of Ligand Transport through Protein Tunnels
25.6.: PrankWeb
4.6.: EnzymeMiner & SoluProt: mining of soluble enzymes
4.6.2021 at 9:30 Jiří Hon from FNUSA-International Clinical Research Center will talk about EnzymeMiner & SoluProt: mining of soluble enzymes
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 nr database. SoluProt is a machine-learning method for prediction of soluble protein expression in E. coli integrated in EnzymeMiner for prioritization of search hits. EnzymeMiner and SoluProt help to identify novel putative enzymes and facilitate selection of several expressible targets for experimental characterization. These novel enzymes might have successful applications in biosynthetic pathways for the ecological production or degradation of chemical compounds.
11.6.: IRESs, IRESite and HCVIVdb
11.6.2021 at 9:30 Martin Pospíšek from Charles University will talk aboutIRESs, IRESite and HCVIVdb
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 tool for searching of specific RNA structure in the library of different RNA structures including an attempt to use this tool for finding of IRES-like structures in the human genome.
18.6.: CaverDock: Analysis of Ligand Transport through Protein Tunnels
18.6.2021 at 9:30 Ondřej Vávra from FNUSA-International Clinical Research Center will talk about CaverDock: Analysis of Ligand Transport through Protein Tunnels
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 needs to be studied. We present CaverDock tool, implementing a novel method for analysis of transport processes. The method is based on modified molecular docking algorithm of AutoDock Vina. The output is ligand’s trajectory and energy profile of the transport process.<
25.6.: PrankWeb
25.6. 2021 at 9:30 Marian Novotný from Charles University will talk about 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.