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Structural Bioinformatics of Protein Interactions



Dr. Olga Kalinina

Protein three-dimensional structure is the key to understanding protein function in a biological system. The constant improvement of the experimental techniques for the protein structure determination leads to an exponentially growing number of resolved structures of individual proteins and protein complexes, which open new avenues for their analysis and comparison. The group of Dr. Olga Kalinina develops novel methods that combine information on protein structures and their evolution to gain new insights into how proteins work, and how the changes in their sequence may affect their function.



Our projects

Our research interests include evolution of mechanisms that confer protein interaction. Of particular interest to us are viruses, because their unique biology and importance for the public health render them ideal models for our studies. The high evolutionary rate of many viruses allows them to evolve measurable phenotypic traits in little time. Additionally, viruses engage in an extensive and highly regulated network of interactions with the host cell.

There are several areas of interest in this respect:

  • The change of free binding energy of ligands upon point mutations in the virus protein
  • Evolution of binding interfaces in interactions between viral-viral and viral-host proteins
  • Modelling the emergence of resistance towards anti-viral drugs
  • Modelling specificity of virus-host interactions



The evolution of viruses of the large scale is also a topic of interest in our group. We are working on detection of abnormal evolutionary patterns in the viral proteome, such as horizontal gene transfer events into viral families, or gene exchange between distantly related viral families. We are also interested in a deeper reconstruction of phylogenies between viral families based on protein structure comparison.

We also have interests not related to viruses. Some of these projects are:

  • Specificity within eukaryotic signalling cascades
  • Modelling of drug-resistance conferring mutations in pathogenic bacteria