Avidin related protein 2 shows unique structural and functional features among the avidin protein family

Background  

The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin.     

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites

We developed the computer system SITEVIDEO for analysis andrecognition of the functional sites in DNA and RNA molecules.It reveals contextual features essential for site function andthus enable the user to design efficient methods for recognitionof the functional sites. We mainly considered only quantitativecharacteristics reflecting the uneven distribution of oligonucleotidesin the sequences of functional sites of interest. The approachsuggested makes use of available information about the hierarchicalorganization of the functional sites, and ensures highly preciseprediction of the sites. The present analysis is concerned withthe human donor and acceptor splice sites. A method for recognizingthese sites in the sequences with an accuracy of 90% was developed.     

GeneExpress: an integrator for databases and computer systems accessible by the Internet and intended for studying eukaryotic gene expression

We have developed GeneExpress that is the WWW-oriented integrator for the databases and systems supporting the investigation of gene expression. The total number of the Web-based resources integrated is 30. The database GeneNet on molecular events forming gene networks was assigned its integrative core. To navigate all these WWW-available resources, the SRS, HTML, and Java viewers were developed, http:@wwwmgs.bionet.nsc.ru/systems/GeneExpress/.     

Identification of dominant signaling pathways from proteomics expression data

The availability of the results of high-throughput analyses coming from ‘omic’ technologies has been one of the major driving forces of pathway biology. Analytical pathway biology strives to design a ‘pathway search engine’, where the input is the ‘omic’ data and the output is the list of activated or dominant pathways in a given sample. Here we describe the first attempt to design and validate such a pathway search engine using as input expression proteomics data. The engine represents a specific workflow in computational tools developed originally for mRNA analysis (BMC Bioinformatics 2006, 7 (Suppl 2), S13). Using our own datasets as well as data from recent proteomics literature we demonstrate that different dominant pathways (EGF, TGF_β, stress, and Fas pathways) can be correctly identified even from limited datasets. Pathway search engines can find application in a variety of proteomics-related fields, from fundamental molecular biology to search for novel types of disease biomarkers.