Research
Our group develops innovative methods for studying the structure and dynamics of biomacromolecules. These include bioinformatics approaches to exploit the relationship between a sequence and a structure as well as coarse grained and multiscale modelling. The current research is focused on:
Computational analyses of biomolecules
BioShell software package, that has been started in 2006, is a comprehensible set of tools for structural bioinformatics. The most recently published version 3.0 of the package provides Python bindings to C++ modules of BioShell.
Interatomic interactions
The newest version allows also to detect and analyse interatomic interactions, such as hydrogen bonds, Van der Waals and stacking interactions.
![](https://bioshell.pl/wp-content/uploads/2020/06/1.png)
![](https://bioshell.pl/wp-content/uploads/2021/02/az-bioshell.png)
Coarse grained modelling of proteins
In coarse-grained models, a group of atoms , such as an amino acid side chain, a residue or a small molecule, is substituted with a single interaction center – united atom. Numerous models have been proposed in the past few decades, that differ in how they represent all-atom molecules and how they describe interactions.
SURPASS model
in the Single United Residue per Pre-Averaged Secondary Structure fragment (SURPASS) model a single coarse-grained atom corresponds roughly to an amino acid residue.
Project has been supported by:
2018/29/B/ST6/01989 NCN research grant:
,,Novel combination of Rosetta method with SURPASS coarse grained model into a multiscale protocol for modelling proteins and their complexes''.
The project has been realized at Warsaw University.