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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(More)
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(More)
PDBSiteScan is a web-accessible program designed for searching three-dimensional (3D) protein fragments similar in structure to known active, binding and posttranslational modification sites. A collection of known sites we designated as PDBSite was set up by automated processing of the PDB database using the data on site localization in the SITE field.(More)
BACKGROUND The translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nucleotide context. However, the fraction of eukaryotic mRNAs with the start codon in a suboptimal context is relatively large. It may be(More)
MOTIVATION The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the(More)
We have developed PROF_PAT, a database of patterns, constructed for groups of related proteins and designed to maximize representation of amino acid sequences from the SWISS-PROT database. The purpose of the current study was to demonstrate that PROT_PAT is not only as good as known analogs but surpasses them in some features. 10938 new amino acid sequences(More)
Computer system mRNA-FAST (mRNA--Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with(More)
The structure of the Transcription Regulatory Regions Database (TRRD) and the principles of considering transcription regulation of eukaryotic genes in TRRD are concerned. Formal description of the structural and functional organization of the regulatory gene regions is illustrated with examples. By now, TRRD is based on 3500 original works and contains(More)
We report an integrative technology for molecular biology studies in the field of transcription regulation by using Internet. A set of databases, programs, and systems are included into WWWMGS Web server. For example, the use of TRRD database information for site prediction is described. Using this method, the computer system SeqAnn was developed. The(More)