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:
BioShell package development
BioShell is an open-source package for processing biological data, particularly focused on structural applications. The package provides parsers, data structures and algorithms for handling and analyzing macromolecular sequences, structures and sequence profiles. The most frequently used routines are accessible by a set of easy-to-use command line utilities for a Linux environment. The full functionality of the package assumes knowledge of C++ or Python to assemble an application using this software library.
Single United Residue per Pre-Averaged Secondary Structure fragment is a coarse-grained low resolution model for protein simulations. Its design has been based on the statistical analysis of structural regularities characteristic for protein systems. The ongoing development of the SURPASS model leads towards modelling of multi-chain systems in perioduc boundary conditions.
P450 protein family maining & modelling
Cytochromes P450 (CYPs) are a superfamily of enzymes containing heme as a cofactor that function as monooxygenases. Currently we know approximately 200 000 members of the family, but the total number of sequences most likely exceeds a million. Our group is involved in P450 classification, modelling of structures and ligand docking.
Our work is primarily focused on development of research software for macromolecular structure modelling, analysis and visualization. We develop BioShell software package, SURPASS model and VisuaLife library for scientific visualization. We also actively participate in the development of Rosetta software package.
Most recent works from our laboratory
Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks
Mohammad N. Saqib, Justyna D. Kryś, Dominik Gront
An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species
Malinga, N.A.; Nzuza, N.; Padayachee, T.; Syed, P.R.; Karpoormath, R.; Gront, D.; Nelson, D.R.; Syed, K.
Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria.
Msweli, S.; Chonco, A.; Msweli, L.; Syed, P.R.; Karpoormath, R.; Chen, W.; Gront, D.; Nkosi, B.V.Z.; Nelson, D.R.; Syed, K.
Int. J. Mol. Sci. 2022
Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters
Nkosi, B.V.Z.; Padayachee, T.; Gront, D.; Nelson, D.R.; Syed, K.
Int. J. Mol. Sci. 2022
Members of our laboratory teach a few courses, that are quite relevant to our research: ,,Molecular Modelling” (both in English and Polish), ,,Bioinformatics”, ,,Bioinformatics II” and ,,Structure of Polymers and Biopolymers” – all of them in Polish only.
Special courses in english, such as ,,Introduction to Programming” or ,,Bioinformatics” are opened for Erasmus students upon request.
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.
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