We develop software tools that focus mainly on analysing the 3D structure of proteins, ligands, protein fragments, and whole protein families.
Our research is focused on analysing the 3D structure of proteins, protein fragments, and whole protein families.
Biomacromolecular structural data from over seven decades of intensive research are a precious and scientifically vital resource. More than 200,000 experimentally determined three-dimensional structures of biological macromolecules are available from the open-access Protein Data Bank (PDB). The PDB archive continues to grow in terms of the number of new entries and the complexity and size of deposited structures. These structural data enabled the establishment of rich datasets describing individual protein families. The data provide us with a robust basis for examining individual proteins and protein families, discovering their essential parts, and understanding their structure-function relationships.
Our research concentrates on visualisation, validation, annotation, fragment detection, and characterisation of proteins and protein families. We also develop software tools for performing these types of analyses.
The main areas of our research:
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Mol*
High-performance graphics and data handling of the Mol* Viewer allow users to simultaneously visualise up to hundreds of (superimposed) protein structures, play molecular dynamics trajectories, render cell-level models at atomic detail with tens of millions of atoms, or display huge models obtained by I/HM such as the Nuclear Pore Complex.
Mol*VS
Mol* Volumes & Segmentations (Mol*VS) is a Mol* Viewer extension which adds support for large scale volumetric data & their segmentations. Building on the existing Mol* ecosystem, this extension allows seamless integration of biomolecular data from cellular to atomic scale.
OverProt
OverProt creates an overview of secondary structure elements in protein families. For each protein family from the CATH database, a secondary structure consensus is available, showing the characteristic helices and β-sheets of the family.
2DProts
2DProt contains 2D diagrams of secondary structures of domains in protein biomacromolecules. Offered diagrams visualize relative distance between single secondary structure elements, as well as position of amino acids that comprise each element in the sequence of the domain.
ValidatorDB
Database of validation results for ligands and non-standard residues in the Protein Data Bank.
MotiveValidator
MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).
ValTrendsDB
Database of biomacromolecular structure validation trends.
MOLEonline
MOLEonline web interface provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.
ChannelsDB 2.0
ChannelsDB 2.0 is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank and AlphaFill / AlphaFold databases. As such, it is a unique service for channel-related analyses.
PatternQuery
PatternQuery is an interactive, user-friendly, and platform independent web service enabling the user to effectively define, extract, and analyze structural patterns or biomolecular complexes using the PatternQuery language.
αCharges
AlphaCharges (αCharges) is a web application for the calculation of partial atomic charges on protein structures predicted by the AlphaFold2 algorithm and deposited in the AlphaFoldDB database.
Atomic Charge Calculator II
Atomic Charge Calculator II (ACC II) is an application for fast calculation of partial atomic charges. It features 20 empirical methods along with parameters from literature.
SecStrAnnotator
SecStrAnnotator is a software tool for annotation (naming) of secondary structure elements (SSEs), namely α-helices and β-strands, in protein structures. The SSE annotation is template-based, meaning that a structurally similar template protein with annotated SSEs must be provided.