Services

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

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.

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

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

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

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).

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

Universal Catalog Database for biological findings

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

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

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

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.

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.

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

Structural and physico-chemical interpretation of QSAR models

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.

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.

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).

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.

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.

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.

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.

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

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

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

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.

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

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.

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

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

Template-based RNA secondary structure visualization.

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

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

Atlas of Protein Hydration

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

Integrated Database of Small Molecules

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

A tool for analyzing BLAST search output for RNA sequences.

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

Czech COVID-19 genomics portal

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.

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

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

Tool to infer or validate genetic networks based on expression time series data.

a plugin for importing and handling time series and other forms of repeated measurements data in Cytoscape

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.

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.

Atomic Charge Calculator II (ACC II) is a web application for fast calculation of partial atomic charges.

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

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.

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.

Haplotype analyzer for the Czech population.

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.

REXdb: a reference database of transposable element protein domains

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

GOLEM is a web-based application that can be used to display the distribution of regulatory gene motifs within gene sequences in selected plants.

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

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

Lite chemoinformatics framework in Python.

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

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.

A web database of biomacromolecular structure validation trends.

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.

An interactive web viewer of metadynamics results.

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

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

Location and basic characterization of channels in molecular structures.

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

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

A proteomics web database.

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

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

Human endogenous retroviruses database.

A web application for RNA structure comparison.