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Professional activity
Prediction Center


Bioinformatics (2000-present)

  • analysis, classification and prediction of protein structures from amino-acid sequence
    • development of the method of local descriptors of protein structure
    • comparison of protein structures in non-rigid body regime
    • fold recognition using sequence fingerprints of contacting backbone segments
  • identifying gene regulation mechanisms using supervised machine learning
    • discovering regulatory binding site modules in genes from gene expression similarities
  • detecting protein function based on sequence-derived properties of local substructures
  • predicting enzyme-ligand interactions using local protein substructures
  • predicting inter-residue contacts in proteins
  • evaluation of protein structure prediction
  • evaluation of model quality assessment prediction
  • evaluation of disorder in proteins
  • evaluation of residue-residue contacts in proteins
  • evaluation of cryo-EM models

Mechanics/Applied Mathematics (1988-2000)

  • contact mechanics
    • thermoelastic interaction of anisotropic bodies with uneven surfaces
    • friction influence on stresses in systems of mated anisotropic bodies with uneven surfaces
  • failure mechanics
    • stresses and strains in thermoelastic bodies with cracks
    • analysis of strength and failure loadings in systems of precompressed bodies with local surface defects
  • mechanics of layered bodies
    • influence of anisotropy and interlayer cavities on stresses in systems of mated laminants
  • theory of singular integro-differential equations (SIDE)
    • application to contact problems in thermomechanics
    • development of numerical methods for SIDE solution


  • CASP (Critical Assessment of techniques for protein Structure Prediction)
      Co-organizer, 2004-present
    • development of methods and tools for evaluation of protein models;
    • design and management of the automatic system for data handling;
    • preparation and processing of the data;
    • evaluation and visualization of the results;
    • communication with X-ray crystallographers and NMR spectroscopists;
    • facilitation and coordination of work of the experiment assessors;
    • communication with predictors;
    • development and maintenance of the Prediction Center's website (

  • Cryo-EM Model Challenges
      Organizing Team member, 2016-present
    • development of methods and tools for evaluation of cryo-EM models;
    • preparation and processing of the data;
    • evaluation and visualization of the results;
    • development of the Model Challenge website (

  • Community-wide experiment CASP-Commons (CASP-covid 2020, CASP-NMR 2018)
  • World-wide experiment on continuous assessment of protein models for challenging prediction targets (CASP ROLL, 2011-2016, co-organizer)
  • CASP predictors meetings (CASP5-CASP14, 2000-2020)
  • Public CASP7.5 meeting - Madrid, Spain, April 2008, co-organizer
  • Mutant modeling experiment - September-November 2007, co-organizer
  • Protein model refinement experiment - January-March 2006, co-organizer
  • Public meeting "Perspectives on the state-of-the-art in structure prediction" - New York, May 2006, co-organizer
  • CASP Decoy sets database
  • Ten Most Wanted (proteins)
  • Reviewer for journals
    • Proteins:Structure, Function and Bioinformatics (Associate editor)
    • Bioinformatics
    • Nucleic Acids Research
    • Nature Communications
    • Nature Methods
    • Nature Scientific Reports
    • Briefings in Bioinformatics
    • PLOS One
    • PLOS Computational Biology
    • PLOS Biology
    • BMC Structural Biology
    • BMC Bioinformatics
    • BMC Biology
    • ACS Omega
    • Journal of Biomolecular Structure and Dynamics
    • Journal of Chemical Information and Modeling
    • IEEE/ACM Transactions on Computational Biology and Bioinformatics
    • Current Protein and Peptide Science
  • Program committee member for conferences and scientific meetings