Research Areas

The problem of the ‘evolutionary space of a gene’ or ‘sequence space (both protein and nucleotide)’ has been known for quite some time. However, the most well-known works on this topic (using the query ‘sequence space’ in PubMed) appeal to the purely evolutionary aspects of this problem (evolutionary and adaptive landscapes). However, the problem of sequence space also has a purely geometric aspect, which involves the correct embedding of pairwise evolutionary distances from a corresponding matrix into a metric/non-metric space.

Initial research attempts were carried out by the laboratory team about eight years ago; however, the sketch of the evolutionary space and, in particular, the methods used in its construction were not sufficiently accurate. Nevertheless, the problem of uncovering hidden evolutionary patterns, which possess obvious fundamentally important properties, remains highly relevant.

Within the framework of this project, the task of embedding a pairwise distance matrix into an adequate space, followed by visualisation, is being solved with the highest possible mathematical precision. The work is being carried out in collaboration with the All-Russia Research Institute for Agricultural Microbiology, the Research Institute of Influenza, as well as with scientists from the University of Pisa and the University of Tübingen.

The laboratory is developing methods for the rapid and accurate prediction of protein mobility using artificial neural networks. The essence of the method lies in reducing the computational load and increasing the performance of calculations when studying the dynamics of complex molecular systems involving one or more large proteins.

A separate objective is the task of modelling protein structures in the absence of experimentally resolved three-dimensional models of their structure, or in the presence of fragmented data that does not reveal a full-size model of the protein.

This area of the laboratory's work is applied in nature. Within its framework, practical tasks related to the molecular design of physiologically active substances with target-specific properties are addressed. To achieve this, a comprehensive multi-level approach is employed, utilising a wide range of molecular modelling methods, from single-step docking to molecular dynamics, metadynamics, and FEP+.

All research is interdisciplinary and is closely integrated with the experimental work of leading scientific centres: synthetic chemists from St Petersburg State University (SPbSU) and the St Petersburg State Institute of Technology (Technical University) carry out the synthesis of the proposed compounds, while biologists from Pavlov First St Petersburg State Medical University and other partner institutions conduct their biological validation.

The practical work is focused on several socially significant therapeutic areas: antibiotics, antiviral agents, antitumor drugs, therapy for diabetes and other metabolic disorders, and inducers of cell pluripotency.