Computer Program for Detection and Analyzing the Porin-Mediated Antibiotic Resistance of Bacteria.

Unlabelled: was to develop a new software tool for identifying gene mutations that determine the porin-mediated resistance to antibiotics in gram-negative bacteria and to demonstrate the functionality of this program by detecting porin-mediated resistance to carbapenems in clinical isolates of .

Materials And Methods: The proposed algorithm is based on searching for a correspondence between the reference and the studied genes. When the sought nucleotide sequence is found in the analyzed genome, it is compared with the reference one and analyzed.

In silico design of high-affinity ligands for the immobilization of inulinase.

Using computer modeling, virtual screening of high-affinity ligands for immobilization of inulinase - an enzyme that cleaves inulin and fructose-containing polymers to fructose - has been performed. The inulinase molecule from Aspergillus ficuum (pdb: 3SC7) taken from the database of protein structures was used as a protein model and the target for flexible docking. The set of ligands studied included simple sugars (activators, inhibitors, products of enzymatic catalysis), as well as high-molecular weight compounds (polycation and polyanion exchange resins, glycoproteins, phenylalanine-proline peptide, polylactate, and caffeine).

Structural and dynamic properties of thymopoietin mimetics.

We propose a hypothesis that the T-cell receptor is a possible target of thymic hormones. We modelled the conformational dynamics of thymopentin and its structural variants in solution, as well as the interactions of these short peptides with the proposed molecular target. Thymopentin is a five-amino-acid fragment of the thymic hormone thymopoietin (residues 32 to 36) that reproduces the immunomodulatory activity of the complete hormone.

[Experience in simulating the structural and dynamic features of small proteins using table supercomputers].

The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, "table supercomputers", using distributed calculations by the CUDA technology.

[On possible influence of different pathways of binding of amides with water on the "pyramidalization" of nitrogen valence bonds of peptide groups].

With the aim to study solvation effects in peptide structure organization, the energy of different types of hydration in simple amines and amides has been analyzed. It was shown based on the quantum-chemical DFT and PM3 calculations of amino derivatives CH3-(CH2)3-NH2, (CH3)2-NH, CH3-NH2, NH3, CH2=CH-NH2, H-CC-NH2, O=C(CH)3-N(CH3)2, O=C(CH3)-NH(CH3), O=C(CH3)-NH2, O=CH-N(CH3)H, and O=CH-NH2 that: (1) in the given set of molecules, the proton acceptor N..

[Torsion lability of the O=C-N-H fragment in single dipeptide molecules of L-amino acids].

On the basis of ab initio MP2 and semi-empirical PM3 quantum-chemical calculations the bistability of the nonplanar O=C-N-H fragment in the structure of simple amides and dipeptides is discussed. The influence of the nature of amino acids on the structural polymorphism of the peptide group in dipeptides is shown.