Software
AggreProt
The AggreProt web server is a user-friendly interface to our recently developed predictor targeting protein aggregation. The predictor consists of an ensemble of deep neural networks that were trained on a collection of amyloidogenic hexapeptides WaltzDB. Amyloid aggregation is characteristic of important neurodegenerative human diseases, such as Alzheimer’s or Parkinson’s. We demonstrated the ability of our predictor to detect aggregation-prone regions in non-amyloid aggregation on the haloalkane dehalogenase and luciferase. AggreProt web server requires minimal input and presents comprehensive results.Academic and commercial users • 1st Publication
PredictONCO 1.0
PredictONCO 1.0 is a unique web server for the analysis of the effects of mutation on oncologically important proteins. The server is designed to assess the effects on sequential and structural properties of a protein and apply a virtual screening method to suggest possibly interesting drugs for further treatment. PredictONCO relies on predictions of state-of-the-art tools combined with knowledge from established and popular databases. Its user interface was carefully designed with respect to the target community of medical practitioners and researchers to display only the important values and pointers for their decision. As their decisions are often hindered by lack of time, the whole server was designed to be as fast as possible and to re-use as many pieces of data as possible.
LoopGrafter
LoopGrafter is a web-based application designed to provide guidance in the process of transplanting loops in between homologous, structurally-related proteins. The server provides a step-by-step procedure in which the user can successively calculate loops and their geometries in the two input proteins, assess their similarities and dynamics using elastic network models, explore correlated motions among loops, and finally propose a number of loops to be transplanted. LoopGrafter calculates all possible insertion points that produce different chimeric protein sequences for any combination of the selected loops. Finally, three-dimensional structure models of the grafted proteins are built using Modeller and scored using Rosetta FastRelax. All the models and their sequences can be interactively visualized and independently downloaded.Academic and commercial users • 1st Publication
SoluProtMutDB
SoluProtMutDB is a comprehensive, manually curated database of the protein solubility data for single- and multi-point mutants. The goal of the database is to collect the reported evidence of solubility changes upon mutations from published sources to guide future protein engineering efforts in producing soluble protein variants. We are providing manually curated and reliable data in the standardized format pre-processed for machine learning applications.
FireProtDB 1.0
FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. This database combines the published datasets, the data extracted from the recent literature, and the measurements collected in our laboratory. The graphical user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or a mutation and (ii) the construction of highly customized, machine learning-friendly datasets using advanced searching and filtering.Academic users • Commercial users • 1st Publication
FireProtASR 1.0
FireProtASR is a web server for an automated calculation of ancestral sequences. FireprotASR allows users to perform ancestral sequence reconstruction starting from a single protein sequence without prior knowledge of the bioinformatics tools and the biological system of interest. The pipeline first compiles a dataset of catalytically similar protein sequences, aligns them, construct their phylogenetic tree, and finally reconstruct ancestral sequences together with ancestral gaps. It also allows users to utilize their own data and start from a different points of the calculation.Academic users • Commercial users
CAVER Web 1.0
Caver Web is an interactive web server for comprehensive analysis of protein tunnels and channels as well as the ligands’ transport within a single graphical user interface. The whole process of tunnel detection and analysis of ligand transport is facilitated by automated guidance procedures which assist the users to correctly set up the calculation leading to accurate and biologically relevant results. The first part of the workflow is tunnel detection and visualization using the gold standard Caver. The second part of the workflow analyses ligand transport by CaverDock. Multiple ligands can be provided as the files with coordinates, ZINC database accession codes or by drawing the structure in molecule editor. CaverDock balances computational demands (2-20 min/job) and accuracy.Academic users • Commercial users • 1st Publication
SoluProt 1.0
SoluProt is a web application for a prediction of protein solubility from protein primary sequence. A solubility score calculated for an entire protein sequence is useful for the prioritization of protein sequences selected for the laboratory production in genomic projects. The predictor is in its current version based on the random forest regression model and employs 36 sequence-based features, e.g., amino acid content, predicted disorder, alpha-helix and beta-sheet content, sequence identity to PDB and several aggregated physico-chemical properties. SoluProt currently achieves the accuracy of 58.2% and is a subject to further active development.Academic users • Commercial users
EnzymeMiner 1.0
EnzymeMiner is a web application for automated and periodical mining of interesting sequences in genomic databases. The server utilizes a number of sequence and structural bioinformatics tools for the identification of protein-coding genes with conserved catalytic residues presumably catalyzing a defined enzymatic reaction. The functional diversity of mined hits is secured by the prediction of protein tertiary structures, analysis of protein cavities and access tunnels, modelling of enzyme-substrate complexes and prediction of their reactivity.Academic users • Commercial users • 1st Publication
CalFitter 2.0
CalFitter is a computational tool for an analysis and fitting of calorimetric protein melting curves obtained from differential scanning calorimetry (DSC) measurements. The application allows simultaneous global fitting with various scan rates and reheating using 10 different models of unfolding. Apart from the heat capacity curve, each model provides a population of intermediates versus temperature, fitted parameter values, and respective confidence intervals of the fitting. The program provides a means to export the analysis into Excel as well.Academic users • Commercial users • 1st Publication • 2nd Publication • 3rd Publication
CaverDock 1.0
CaverDock is a new tool for extremely rapid analysis of transportation processes in proteins. It models the transportation of a ligand (a substrate, a product, an inhibitor, a co-factor or a co-solvent) from the outside environment into the binding site and vice versa. The tool implements a novel algorithm based on molecular docking and is able to produce contiguous ligand trajectories and estimations of the binding energy along the pathways. CaverDock uses Caver for the pathway identification and a heavily modified Autodock Vina as the docking engine. The tool is much faster than molecular dynamics (2-20 min per job) and is also suitable for virtual screening.Academic users • Commercial users • 1st Publication • 2nd Publication
FireProt 1.0
FireProt provides a robust computational strategy for predicting highly stable multiple-point mutants. It combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt integrates sixteen computational tools, utilizing both sequence and structural information. The web server provides users with a one-stop-shop solution for the design of thermostable proteins, designed by three strategies: (i) an evolution-based approach, utilizing a back-to-consensus analysis; (ii) an energy-based approach, using conservation, correlation, and energy and (iii) a combined approach.Academic users • Commercial users • 1st Publication • 2nd Publication
PredictSNP
PredictSNP1 is an ensemble-based classifier for a prediction of the effect of amino acid substitutions and their prioritization for experimental characterization. It combines six well-established computational methods (MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP) with a two-level weighted consensus approach to provide a more accurate and robust alternative to the predictions delivered by the individual tools. The predictions are complemented with experimental annotations from the Protein Mutant and the UniProt databases. PredictSNP2 extends the scope to nucleotide substitutions and enables the identifications of disease-related variants within the whole genome. Similarly to PredictSNP1, the results of the five existing best-performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) are combined with a two-level weighted consensus approach. To provide a comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases.Academic users • Commercial users • 1st Publication • 2nd Publication
HotSpot Wizard 3.0
HotSpot Wizard is a web server for automated identification of ‘hot spots’ and design of smart libraries for engineering protein stability, catalytic activity, substrate specificity and enantioselectivity. HotSpot Wizard implements four different established protein engineering strategies, enabling users to selectively target sites affecting protein stability and catalytic properties. The server should be useful for protein engineers interested in exploring the structure of their favourite protein and for the design of mutations in site-directed mutagenesis and focused directed evolution experiments.Academic users • Commercial users • 1st Publication • 2nd Publication • 3rd Publication
CAVER 3.0
CAVER is a gold standard for identification and characterization of tunnels and channels in macromolecular structures. The new version enables automatic analysis of transport pathways in large ensembles of protein conformations. The analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and the elucidation of the structural basis of tunnel gating. CAVER paves the way for the study of important biochemical phenomena in the areas of molecular transport, molecular recognition and enzymatic catalysis. The software is available as a multiplatform JAVA command-line application or a PyMol plug-in.Academic users • Commercial users • 1st Publication • 2nd Publication
CAVER Analyst 2.0
CAVER Analyst is a tool for a calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphical user interface for setting up the calculation and an interactive exploration of identified tunnels/channels and their characteristics. Novel integrated algorithms allow for an efficient analysis and data reduction in large protein structures and molecular dynamics simulations in AMBER, GROMACS and CHARMM formats. It offers a possibility to design one or more mutations in selected positions. CAVER Analyst is a freely available multi-platform software written in JAVA.Academic users • Commercial users • 1st Publication • 2nd Publication