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The paper presents the system-“Exactus Expert”—search and analytical engine. The system aims to provide comprehensive tools for analysis of large-scale collections of scientific documents for experts and researchers. The system challenges many tasks, among them full-text search, search for similar documents, automatic quality assessment, term and definition extraction, results extraction and comparison, detection of scientific directions and analysis of references. These features help to aggregate information about different sides of scientific activity and can be useful for evaluation of research projects and groups. The paper discusses general architecture of the system, implemented methods of scientific publication analysis and some experimental results.