Online Tools

From Bioinformatics Group

Following section comprises services referenced in journal articles along with individual student projects. You are free to use them for non-commercial purposes.


Protein Knot Finder

Protein Knot Finder: a server for recognizing and categorizing protein knots. Occurrence of knots was assumed to be impossible in protein structures until, unexpectedly, first structures containing knots were deposited in RCSB PDB. The server is capable of identifying whether in a given protein structure there is a knot, i.e. a structural motif that prevents the backbone from becoming a straight line when pulled by its termini.

Go to the website of [Protein Knot Finder]

EarlyStage and Vear

EarlyStage: a server for creation of the early stage intermediate structure in protein folding. A significant number of proteins have been found experimentally to fold via a two-state process in which only the fully unfolded and native states are ever populated. Our approach assumes two states in the protein folding process: early-stage and late-stage folding. The two-states are closely related with the idea of the reduced conformational space for early-stage protein folding. The complete conformational space is available after reaching the proper conformation determined in a first step of folding. The existence of the first step determines to some extent the search for the final native conformation.

Go to the website of [EarlyStage]

Vear: a local geometry-based structural viewer for polypeptides. A unified description of protein structure is essential when structural similarity judgement, motif transitions or general folding are considered. In the applied approach, an assumption that all polypeptide chain conformations can be classified as helix-derived coerced invention of a new method of protein structure description based on geometrical parameters: radius of curvature R and dihedral angle between two consecutive peptide bond planes V. Developed basing on the model pentapeptides it helped to determine the general conformational subspace that turned out to be more useful than traditional φ/ψ mapping.

Go to the website of [Vear].

ActiveSite and Reveal

ActiveSite: a server for binding site recognition. The model oriented on localization of areas responsible for ligand binding or protein-protein complex creation is based on characteristics of spatial distribution of hydrophobicity in a protein molecule: It is assumed that hydrophobicity changes from protein interior (maximal) to exterior (close to zero) according to the three-dimensional Gauss distribution (fuzzy oil-drop model). It is generally accepted that the core region is not well described by a spheroid of buried residues surrounded by surfaces residues due to hydrophobic channels that permeate the molecule. Therefore the simple comparison of theoretical (idealized according to Gauss function) and empirical spatial distribution of hydrophobicity in protein gives the opportunity to identify the regions with high deviation versus the ideal model. Those regions recognized by high hydrophobicity density discrepancy seem to reveal functionally important sites in proteins.

Go to the website of the server [ActiveSite]

Reveal: a molecular surface viewer for binding site recognition.

Go to the molecular surface viewer webpage [Reveal]


Calculation of Z-coefficient in contingency tables. This on-line tool measures level of association between groups of events in a population. We make use of coefficient Z - the unordered and asymmetrical dependency measure.

Go to the website of [ZCoeff]

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