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Your search keyword '"Dmitry A. Grigorovich"' showing total 3 results
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3 results on '"Dmitry A. Grigorovich"'

1. CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

Author

Viktoriya V. Lavrekha, Victor G. Levitsky, Anton V. Tsukanov, Anton G. Bogomolov, Dmitry A. Grigorovich, Nadya Omelyanchuk, Elena V. Ubogoeva, Elena V. Zemlyanskaya, and Victoria Mironova

Subjects
multi-omics data integration, DAP-seq, proximal promoters, RNA-seq, transcription factor binding profiles, Plant culture, SB1-1110
Abstract

Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.

Published
2022
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2. PDBSite: a database of the 3D structure of protein functional sites

Author

N. A. Kolchanov, S. S. Pintus, Vladimir A. Ivanisenko, and Dmitry A. Grigorovich

Subjects
Models, Molecular, Binding Sites, Database, Protein Data Bank (RCSB PDB), A protein, Proteins, computer.file_format, Articles, Biology, Protein Data Bank, computer.software_genre, Functional description, Protein Structure, Tertiary, Protein structure, Carrier protein, Proteins metabolism, Mutation, Genetics, Humans, Binding site, Tumor Suppressor Protein p53, Databases, Protein, computer, Software
Abstract

The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein–protein, protein–DNA and protein–RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure. The PDBSite is updated after each new PDB release.

Published
2004

3. SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition

Author

Evgenii E. Vityaev, Dmitry A. Grigorovich, Dmitry Oshchepkov, Tamara M. Khlebodarova, and Elena V. Ignatieva

Subjects
Genetics, Internet, Binding Sites, HMG-box, Context (language use), Sequence alignment, Computational biology, Articles, DNA, Sequence Analysis, DNA, Biology, Regulatory Sequences, Nucleic Acid, DNA binding site, chemistry.chemical_compound, User-Computer Interface, chemistry, Nucleic Acid Conformation, Binding site, TRANSFAC, Transcription factor, Sequence Alignment, Software, Transcription Factors
Abstract

The local DNA conformation in the region of transcription factor binding sites, determined by context, is one of the factors underlying the specificity of DNA-protein interactions. Analysis of the local conformation of a set of functional DNA sequences may allow for determination of the conservative conformational and physicochemical parameters reflecting molecular mechanisms of interaction. The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for >100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a sample proposed by a user. The resource SITECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/.

Published
2004

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