METHODS DEVELOPMENT

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

PROJECTS / COMMUNITY SERVICES (bioinformatics)

• 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 (https://predictioncenter.org)

• 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 (https://model-compare.emdataresource.org)

• 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