[Investigation of the amino acid sequences of open reading frames of the Mycobacterium tuberculosis complete genome with the use of the protein family pattern bank Prof_Pat].

The new version of protein family patterns bank Prof_Pat 1.16 was used to investigate 3924 amino acid sequences of open reading frames of Mycobacterium tuberculosis strain H37Rv. The similarity to proteins with the known function was confirmed for 2772 amino acid sequences.

Exclusion of HIV epitopes shared with human proteins is prerequisite for designing safer AIDS vaccines.

Background: The safety of a potential AIDS vaccine is an issue that will become critical at later stages of product development and needs to be addressed before it is too late.

Objective: In order to design safer vaccine, the HIV antigens, to be deployed in it, should be free of regions that are either present in human proteins or exhibit pronounced structural similarity to proteins responsible for important physiological functions.

Study Design: The approach is based on the use of an original matrix predicting the antigenic similarity of amino acids.

[Bank of samples from the Prof_Pat protein family, assessment of efficacy].

The PROF_PAT protein pattern database has been created and maintained so as to comprise the maximal number of the SWISS-PROT + TrEMBL proteins as patterns. The present paper describes some characteristic features of PROF_PAT to assist the potential user. New amino acid sequences (10938) from the SWISS-PROT database have been analyzed to determine the boundary values of the "score" parameter to distinguish random and significant similarities.

[Determination of glycyrrhizic acid binding sites by a phage display method].

Phages that expose peptides specifically interacting with glycyrrhizic acid (GA) were selected from a phage peptide library by affinity selection and ELISA. Amino acid sequence analysis of the selected peptides and human proteins with the SIM program revealed homology to tyrosine protein kinases, serine/threonine protein kinases, tyrosine phosphatases, and some receptors. Analysis of the peptide and virus protein sequences with the BLAST program showed that GA has affinity for various surface proteins of several human viruses such as HIV-1, hepatitis C virus, and herpesviruses.

[Searching for local similarities between HIV-1 and human proteins. Application to vaccines].

A method for identification of fragments with a high local similarity to human proteins within potentially immunopathogenic regions of HIV-1 proteins was developed. The method is based on the use of an original matrix of antigenic similarity of amino acids. The regions, whose fragments are frequent in human proteins, and regions, exhibiting a high similarity to the proteins responsible for important physiological functions, were identified in HIV-1 proteins.