Services

Access to ELIXIR CZ services, tools and databases, is provided by our partner institutions in an open access format. Some of the services are completely available without authentication, while others require a necessary level of authentication.  The Access via ELIXIR AAI supports easy registration, but also supports levels of strong authentication necessary for sensitive data access.

ELIXIR CZ operates an infrastructure of computing and storage resources. Access policy, terms of use and condition here.

Acknowledgement

Scientific publications resulting from the use of ELIXIR CZ services must include an acknowledgement according to the following pattern:
This work / Part of this work was carried out with the support of ELIXIR CZ Research Infrastructure (ID LM2018131, MEYS CR).

ServicesInstituteSummaryScientific domainsType of servicesscientific_domain_hfiltertype_of_service_hfilter
pyChemInfchemi.muni.cz

Lite chemoinformatics framework in Python.

cheminformatics
ABEEM SolverELIXIR-CZ

Calculates partial atomic charges for small organic molecules, drug-like molecules.

, cheminformatics computational-chemistry
HCVIVdbELIXIR-CZ

A specialized and medically-oriented database of published variations observed within the internal ribosome entry site (IRES) variants in hepatitis C virus.

, , molecular-and-cellular-structures structural-biology virology
TRITONELIXIR-CZ

In silico construction of protein mutants, modelling enzymatic reactions, analysis of essential interactions between the enzyme and its substrate and docking ligand molecules into protein receptors.

computational-chemistry
ValTrendsDB

A web database of biomacromolecular structure validation trends.

data-visualisation
MOLE PyMOL pluginMasaryk University Brno, Czech Republic, Palacký University Olomouc, Czech Republic, ELIXIR-CZ

Plugin for MOLE 2.0 contains extended options for channel starting point automatic detection, for filtering of obtained channels to select only the relevant channels and allows estimation of basic physicochemical properties of channels.

, , , , , , , chemical-biology enzymes enzymes-interactions-and-pathways membrane-and-lipoproteins protein-interactions protein-properties protein-structural-motifs-and-surfaces small-molecules
PatternExplorerMasaryk University, Brno, Czech Republic, ELIXIR-CZ

A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time.

, , , , , , chemical-biology molecular-and-cellular-structures protein-sites-features-and-motifs protein-structural-motifs-and-surfaces small-molecules structural-biology structure-analysistools
Metadyn ViewUniversity of Chemistry and Technology Prague, Czech Republic, ELIXIR-CZ

An interactive web viewer of metadynamics results.

computational-chemistrytools
SiteBinderMasaryk University, Brno, Czech Republic, ELIXIR-CZ

A web based tool for superimposing and analyzing structural fragments in molecules.

, molecular-and-cellular-structures structure-analysistools
HERVdInstitute of Molecular Genetics, AS CR, ELIXIR-CZ

Human endogenous retroviruses database.

, , gene-and-protein-families nucleic-acid-sites-features-and-motifs virologydata
AtomicChargeCalculatorMasaryk University, Brno, Czech Republic, ELIXIR-CZ

A web application for the calculation and analysis of atomic charges in both large biomolecular complexes and small drug-like molecules.

, , , cheminformatics computational-chemistry molecular-and-cellular-structures structure-analysistools
MotiveValidatorMasaryk University, Brno, Czech Republic, ELIXIR-CZ

A web application for validation of annotation of ligands and
residues.

, , , chemical-biology molecular-and-cellular-structures small-molecules structure-analysistools
MOLEPalacký University, Olomouc, Czech Republic, Masaryk University, Brno, Czech Republic

Location and basic characterization of channels in molecular structures.

, , , , , , , chemical-biology enzymes enzymes-interactions-and-pathways membrane-and-lipoproteins protein-interactions protein-properties protein-structural-motifs-and-surfaces small-moleculestools
ValidatorDBMasaryk University, Brno, Czech Republic, ELIXIR-CZ

Database of validation results for ligands and non-standard residues in the Protein Data Bank.

, , , chemical-biology molecular-and-cellular-structures small-molecules structure-analysisdata
PatternQueryMasaryk University, Brno, Czech Republic, ELIXIR-CZ

A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time.

, , , , , , chemical-biology molecular-and-cellular-structures protein-sites-features-and-motifs protein-structural-motifs-and-surfaces small-molecules structural-biology structure-analysistools
SWICZInstitute of Microbiology, Prague, Czech Republic, Biozentrum, Univ. Basel, Switzerland, ELIXIR-CZ

A proteomics web database.

, protein-expression proteomics-experimentdata
HANAUniversity of West Bohemia, Czech Republic

Haplotype analyzer for the Czech population.

, medicine oncology
DecryptorPalacky University Olomouc

Tandem mass spectrometry data analysis of human proteome for presence of point alterations. Subsequently, deduces DNA/mRNA alterations whenever possible.

, , , proteins-and-proteomes proteomics proteomics-experiment rare-diseasestools
SETTERCharles University in Prague, Czech Republic, University of Chemistry and Technology Prague, Czech Republic, ELIXIR-CZ

A web application for RNA structure comparison.

, nucleic-acid-structure-analysis rnatools
RepeatExplorerBiology Centre, CAS, Czech Republic, ELIXIR-CZ

RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering of sequence reads to identify repetitive elements and several additional programs that aid in their annotation and quantification.

, dna-polymorphism mobile-genetic-elementstools
NEEMPNational Centre for Biomolecular Research, Masaryk University, Brno, Central European Institute of Technology, Brno, mail.muni.cz, ELIXIR-CZ

Main function is to perform EEM parameterization. Can be used to efficiently compute EEM charges, validate them against QM ones and to compute the parameter coverage.

computational-chemistry
DolbicoELIXIR-CZ

Database of local biomolecular conformers, stores DNA structural data including the information about DNA local spatial arrangement.

, , dna molecular-and-cellular-structures structural-biologydata
IoM – Interpreter of MassUniversity of South Bohemia, Czech Republic, ELIXIR-CZ

Dedicated for MS data measured in high resolution mode and their interpretation. Primarily oriented on devices developed by the Thermo-Fisher Scientific company.

proteomics-experimenttools
DNASELIXIR-CZ

A web service providing assignment of nucleic acid conformers used in bioinformatic analysis of nucleic acids and protein/DNA interfaces.

nucleic-acid-structure-analysis
MolStar

Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics.

computational-biology
MOLEonlineMasaryk University Brno, Czech Republic, Palacký University Olomouc, Czech Republic, ELIXIR-CZ

Provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.

, , , , , enzymes enzymes-interactions-and-pathways membrane-and-lipoproteins protein-interactions protein-properties protein-structural-motifs-and-surfacestools
DensityServerCEITEC-MU

A web service for streaming slices of 3D volumetric data, most notably the electron density data available in the Electron Density Server (EDS) and electron microscopy imaging data from the Electron Microscopy Data Bank (EMDB).

data-visualisationtools
LiteMolCEITEC-MU

An HTML5 web application for very fast 3D visualization of molecules and other related data. Very fast even for extremely large protein structures.

data-visualisationtools
UniCatDBInstitute of Applied Informatics, Faculty of Science, University of South Bohemia

Universal Catalog Database for biological findings

ecologydata
bio.tools SumCEITEC-MU

Local views over bio.tools data with information about publications and citations.

informaticstools
REXdbELIXIR-CZ

REXdb: a reference database of transposable element protein domains

data
TAREAN

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

tools
WatAA

Atlas of Protein Hydration

, molecular-and-cellular-structures structural-biologydata
P2Rank

Novel machine learning-based method for prediction of ligand binding sites from protein structure.

, , , , cheminformatics molecular-and-cellular-structures protein-interactions protein-sites-features-and-motifs structural-biology
DANTE

Domain based ANnotation of Transposable Elements (DANTE) uses database of Viridiplantae (Metazoa in progress) protein domains derived from transposable elements (Neumann at al 2019) Domains searching is accomplished engaging LASTAL alignment tool. Domains are subsequently annotated and classified using phylogenetic approach.

sequence-analysistools
PrankWeb

Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.

, machine-learning protein-binding-sites
TRAVeLer

Template-based RNA secondary structure visualization.

, , nucleic-acid-structure-analysis rna-seq structure-predictiontools
SPCI

Structural and physico-chemical interpretation of QSAR models

, , chemical-biology chemistry small-moleculestools
2DProts

A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members.

, molecular-and-cellular-structures structural-biologytools
AmtDBInstitute of Molecular Genetics AS CR

This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).

genomicsdata
cpPredictorInstitute of Microbiology AS CR, Charles University in Prague

Template-based predictor of RNA secondary structure. It takes a template RNA secondary structure(s) and a query RNA sequence(s) and generates secondary structure of the query sequence(s) using the provided structure(s) as a template(s). Biological reliability of the generated structures is evaluated in form of z-scores.

, nucleic-acid-structure-analysis rnatools
IRESiteELIXIR-CZ

Our database presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

, , , molecular-and-cellular-structures rna sequence-sites-features-and-motifs structural-biologytools
CaverDockLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic

Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.

, , , , chemical-biology protein-structure-analysis proteins proteins-and-proteomes small-moleculestools
PredictSNP2Loschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.

, , , dna-mutation genomics medical-informatics rare-diseasestools
FireProtLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.

, , , , molecular-and-cellular-structures protein-structure-analysis proteins proteins-and-proteomes structural-biologytools
CAVER WebLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic

A web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.

, , protein-structure-analysis proteins proteins-and-proteomestools
FireProt ASRLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

FireProt-ASR is a web server for an automated calculation of ancestral sequences. Fireprot-ASR allows you to perform ancestral sequence reconstruction starting from a single protein sequence. The pipeline first compiles a dataset of catalytically similar protein sequences, aligns them, construct their phylogenetic tree, and then reconstruct ancestral nodes. It also allows user to input their own data and start from a different point in the pipeline.

, , , phylogenetics proteins proteins-and-proteomes proteomicstools
MOLEonline 2.0

Analysis of access/egress paths to biomolecular channels. A 3D graphical representation of the channel is displayed along with a list of lining residues and biochemical properties.

, , enzymes enzymes-interactions-and-pathways molecular-interactions-pathways-and-networkstools
rPredictorDBELIXIR-CZ

A web database for prediction, analysis and storage of secondary structures of RNAs.

, , nucleic-acid-structure-analysis rnadata tools
BEGDBELIXIR-CZ

Database collects results of highly accurate QM calculations of molecular structures, energies and properties.

computational-chemistrydata
COVd

Czech COVID-19 genomics portal

, bioinformatics-portal virologydata
FireProtDBLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. Proteins find their use in numerous biomedical and biotechnological applications. Naturally occurring proteins usually cannot withstand harsh industrial environments since they have evolved to function under mild conditions. Increasing protein stability is one of the key determinants of protein applicability. The predictive power of the current computational tools is compromised by the limited experimental data that would allow a rigorous training and testing.

, , , , , , , , data-submission-annotation-and-curation genetic-variation literature literature-and-language machine-learning model-organisms protein-folding-stability-and-design proteins proteins-and-proteomestools
OpenPonk

OpenPonk is an open source diagram modeling CASE tool designed for extensibility by various modeling notations and functions.

, software-engineeringinteroperability tools
Data Stewardship Wizard

The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science.

informaticsinteroperability
IDSMIOCB CAS

Integrated Database of Small Molecules

, , chemical-biology cheminformatics compound-libraries-and-screeningdata
MolArt

MolArt (MOLeculAR structure annoTator) – molecular structure annotation and visualization tool.

, , protein-modifications proteins proteins-and-proteomestools
MADORAUniversity of West Bohemia, Czech Republic, ELIXIR-CZ

A web application for processing and visualization of statistics for bone marrow donors registry – especially statistics of donors, executed searches for suitable donor, the typing and harvests before transplantation.

, , medicine oncology translational-medicine
CAVER PyMOL pluginLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic

A PyMOL plugin for identification and analysis of tunnels and channels in static protein structures.

, , protein-structure-analysis proteins proteins-and-proteomes
Amino Acids Interactions Web ServerIOCB CAS

Calculates the residue Interaction Energy Matrix for any protein structure and offers comprehensive analysis of the interfaces in protein–DNA complexes.

protein-folding-stability-and-designtools
ChannelsDBPalacky University Olomouc, Masaryk University Brno

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

, , , , , , , , , , , biophysics chemical-biology enzymes enzymes-interactions-and-pathways literature literature-and-language membrane-and-lipoproteins molecular-and-cellular-structures protein-interactions protein-properties small-molecules structural-biologydata
HotSpot WizardLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

An automated design of mutations and smart libraries for engineering of protein function and stability and annotation of protein structures.

, , , protein-structure-analysis proteins proteins-and-proteomes sequence-sites-features-and-motifstools
PredictSNPLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic, Mayo Clinic, Rochester, New York, United States of America

A consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.

, , , , , , dna-polymorphism genes-and-genomes genetics medical-informatics proteins proteins-and-proteomes rare-diseasestools
CAVERLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic

A tool for identification and analysis of tunnels and channels in static and dynamic protein structures.

, , protein-structure-analysis proteins proteins-and-proteomestools
EnzymeMinerLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

EnzymeMiner identifies putative members of enzyme families or subfamilies and facilitates the selection of promising targets for experimental characterization. Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.

, , , , , , data-mining enzymes enzymes-interactions-and-pathways proteins proteins-and-proteomes proteomics sequence-analysistools
CalFitterLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, Brno University of Technology, Brno, Czech Republic

Unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. Allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways.

, , , , applied-mathematics protein-folding-stability-and-design proteins proteins-and-proteomes proteomicstools
CAVER AnalystLoschmidt Laboratories, Masaryk University, Brno, Czech Republic, International Centre for Clinical Research, Brno, Czech Republic, University of West Bohemia, Plzen, Czech Republic

A tool for interactive visualization and analysis of tunnels, channels and cavities in protein structures.

, , protein-structure-analysis proteins proteins-and-proteomestools
DNATCOInstitute of Biotechnology AS CR, Prague, Czech Republic, ELIXIR-CZ

A web service providing assignment of nucleic acid conformers used in bioinformatic analysis of nucleic acids and protein/DNA interfaces.

, , , dna nucleic-acid-sites-features-and-motifs nucleic-acid-structure-analysis rnatools
GlobalFungi

User interface to data from high-throughput sequencing studies of fungal
communities across terrestrial biomes. Includes sequencing data, sample
locations, sample metadata.

, , , agricultural-science biodiversity evolution-and-phylogeny evolutionary-biologydata
rboAnalyzer

A tool for analyzing BLAST search output for RNA sequences.

functional-regulatory-and-non-coding-rnatools
MolMeDBPalacky University Olomouc

MolMeDB is an open chemistry database about interactions of molecules with membranes.

, , , , biochemistry computational-chemistry literature literature-and-language pharmacologydata