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PROFESSIONAL ACTIVITY at a GLANCE
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
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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
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