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.
A web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.
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.
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.
A tool for interactive visualization and analysis of tunnels, channels and cavities in protein structures.
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 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 identification and analysis of tunnels and channels in static and dynamic 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.
An automated design of mutations and smart libraries for engineering of protein function and stability and annotation of protein structures.
A PyMOL plugin for identification and analysis of tunnels and channels in static protein structures.
MolArt (MOLeculAR structure annoTator) – molecular structure annotation and visualization tool.
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.