BioShell V.3

Bioinformatics tools in your shell

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        Molecular properties

Structure analysis

Biological predictions

Our 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:

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.



Our Publications

Most recent works from our laboratory


Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks

Biomolecules, 2022

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.

Microorganisms, 2022

 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

Group members

Dominik Gront

Dominik Gront

Principal investigator



Joanna Macnar

Joanna Macnar

PhD student


NCN fellow

Justyna Kryś

Justyna Kryś

PhD student


NCN fellow

Dla Studentów

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.

Contact Us

Projekt i realizacja: Media Solutions Group

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