SiteBinder

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

Metadyn View

An interactive web viewer of metadynamics results.

PatternExplorer

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

bio.tools Sum

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

LiteMol

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

DensityServer

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).

MOLEonline

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

IoM – Interpreter of Mass

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

RepeatExplorer

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.

SETTER

A web application for RNA structure comparison.

Decryptor

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

PatternQuery

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

MOLE

Location and basic characterization of channels in molecular structures.

MotiveValidator

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

AtomicChargeCalculator

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

rPredictorDB

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

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.

FireProt ASR

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.

CAVER Web

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

FireProt

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.

PredictSNP2

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.

CaverDock

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.

IRESite

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

cpPredictor

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.

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.

SPCI

Structural and physico-chemical interpretation of QSAR models

TRAVeLer

Template-based RNA secondary structure visualization.

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.

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.

rboAnalyzer

A tool for analyzing BLAST search output for RNA sequences.

DNATCO

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

CAVER Analyst

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

CalFitter

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.

EnzymeMiner

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.

CAVER

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

PredictSNP

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.

HotSpot Wizard

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

Amino Acids Interactions Web Server

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

MolArt

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

OpenPonk

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

FireProtDB

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.