Tatiana Koshlan

• Doctor of Philosophy
• Master's Student at St Petersburg University

This paper presents computational methods for separating oncogenic mutations from neutral mutations of the p53 protein using mathematical processing of the following calculated values for each sample: [Formula: see text], machine learning methods were used to determine the main physical quantities for predicting experimental values [Urea]50%, Kd, [...

This paper proposes a new paradigm for the biophysical concept of measuring the affinity of molecular complexes, based on a matrix representation of biological interactions and subsequent numerical analysis of the stability of this matrix. Our numerical criterion of stability (lg(cond([Formula: see text]))) correlates well with experimental values...

In this paper, the authors present and describe, in detail, an original software-implemented numerical methodology used to determine the effect of mutations on binding to small chemical molecules, on the example of gefitinib, AMPPNP, CO-1686, ASP8273, erlotinib binding with EGFR protein, and imatinib binding with PPARgamma. Furthermore, the develop...

We have developed a method for increasing the stability of amyloid dimers in order to reduce their ability to enter into further biochemical reactions with the formation of toxic oligomers. https://binomlabs.com/ad Numerical calculations are presented in the form of a graphical description, which clearly allows you to see an increase or decrease i...

http://chemical-design.net/naquotinib Naquotinib is an orally available, irreversible, third-generation, mutant-selective, epidermal growth factor receptor (EGFR) inhibitor ASP8273 is a novel, small molecule, irreversible TKI that inhibits EGFR activity in patients with exon 19 deletions, L858R substitutions in exon 21, as well as T790M resistance...

The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 10mer ssRNA.Quantum-mechanical calculation of the interaction of a protein and an RNA molecule taking into account various substitutions of amino acid residues in a protein. The video shows numerical and experimental results.

https://binomlabs.com/ The poster shows the numerical values of the change in the stability of the trimeric complex, taking into account the substitutions of amino acid residues in the antibody, three-dimensional maps make it possible to identify the key amino acid residues with the maximum energy values. Substitutions of amino acid residues in fle...

We do macromolecular calculations for you! All calculations are performed free of charge. You just need to go through a simple registration and send a technical assignment for calculations. The purpose of our software is to obtain preliminary physical data on the interaction of biological molecules, thus the information obtained on the direction of...

Joint analysis of the effect of key mutations in the EGFR protein on binding to JBJ-04-125-02 and AMP A mutant-selective EGFR allosteric inhibitor, JBJ-04-125-02, which as a single agent, can inhibit cell proliferation and EGFR L858R/T790M/C797S signaling in vitro and in vivo. However, increased EGFR dimer formation limits treatment e cacy and lead...

http://chemical-design.net/erlotinib This section provides and describes in detail a numerical method for determining the effect of mutations on binding to small chemical molecules. The method we have developed makes it possible to numerically determine such a parameter as the stability of a complex molecular complex consisting of a protein and a s...

The main goal of our software is to reduce the cost of biochemical experiments by obtaining preliminary information on the interaction of chemical compounds. Software tools for structure analysis of biochemical experiments: Inhibitory potency and binding ability of small molecule Inhibitor dissociation constants for the WT and mutant kinases Enzyme...

This paper has developed and described a detailed method for selecting inhibitors based on modified natural peptides for the SARS-CoV BJ01 spike-glycoprotein. The selection of inhibitors is carried out by increasing the affinity of the peptide to the active center of the protein. This paper also provides a step-by-step algorithm for analyzing the a...

Read More https://binomlabs.com/ad We concluded that the dimers of mutant amyloids form stable and unstable dimeric complexes. If the dimeric complex is stable, then the formation of high molecular weight structures was much slower. This was due to the fact that the stable amyloid peptides were in no hurry to enter into chemical reactions with othe...

We communicate the results of calculations and selection methods, and identify the properties, of inhibitors that block the formation of high-molecular-weight structures from amyloid peptides, with their blocking mechanism explained. We consider in detail the biochemical requirements for, and the criteria and conditions for identification of, inhib...

We present an unconventional method that provides qualitative evaluation of the ability of amyloid peptides to form high-molecular-weight structures and enables us to resolve the stability issue of amyloid dimer complex by means of introduced quantitative descriptors, which are (i) the logarithm of the condition number of matrix of potential energy...

This article describe a detailed method for selecting inhibitors based on modified natural peptides for the SARS-CoV protein spike glycoprotein. The selection of inhibitors is carried out by increasing the affinity of the peptide to the active center of the protein. The article also provides a step-by-step guide to the analysis of affinity of inter...

We can reduce the number of false results in vitro to 87%. Our method will include modification of flexible chains of immunoglobults, stepwise testing of each antibody to antigen, determination of key amino acid residues, range of changes in affinity.Our group is a developer of an innovative method in biology During the first half of the 20th centu...

Let us present the structure of the tetramerization domain of proteins P73. In this section, we carefully study the interaction between different sites, as well as between amino acid residues of polypeptide chains

Thispost is about formula derivation calculating differential entropy for the case of a normal multidimensional distribution and determining its measure of change (¢H) for analysis determining stability dimeric complex.

Database of targeted antitumor therapy for EGFR proteins: HER2 and HER3.Our method is molecularly selective, targeting certain oncogenic molecules, namely the EGFR family of tyrosine kinases, which occupy a significant share in the causes of oncogenic diseases. The diagram shows the percentage of mutations in proteins of the EGFR family in non-smal...

Представлен новый метод, который позволяет анализировать потенциальную энергию электростатического взаимодействия белковых комплексов при точечных заменах аминокислотных остатков с учетом трехмерной структуры комплекса на примере образования димера Nap1-Nap1. Были разработаны карты потенциальной энергии электростатического взаимодействия попарно вз...

Представлен оригинальный метод, позволяющий получить качественную оценку способности амилоидных пептидов образовывать высокомолекулярные структуры, решать проблему стабильности амилоидных димерных комплексов при помощи введенных величин: логарифм числа обусловленности матрицы потенциальной энергии попарного электростатического взаимодействия между...

Представлены расчеты, методы подбора и даны характеристики ингибиторов образования высокомолекулярных структур амилоидными пептидами, дано объяснение их блокирующему действию. Подробно рассмотрены биофизические требования к ингибиторам, критерии и условия их отбора, которые будут блокировать образование амилоидами структур высокого порядка. В качес...

The mathematical model was developed for taking into account the influence of the temperature of an aqueous salt-free solution on the character of dimer formation by different sections of small proteins: H2A–H2B and H3–H4 dimers, and the effect of temperature on various sections of the Bcl-xl protein were studied. The analysis of the numerical calc...

This chapter is devoted to the development of a mathematical model that will allow us to describe the behavior of biological complexes in vitro on the example of the formation of two histone dimers H2A−H2B and H3−H4 from the corresponding monomeric proteins H2A, H2B, H3, and H4 in solutions with different concentrations of monovalent salt. The calc...

In this chapter, two algorithms are developed: Algorithm 1 and Algorithm 2. Algorithm 1 was developed in order to search for the interaction of a polypeptide chain of a full-length protein with short active region. Algorithm 2 was developed to determine the most active sites of interaction between full-length proteins when dimers are formed in the...

This chapter presents a new method that allows one to qualitatively determine the effect of point mutations in peptides on the stability of the formed complex with full-length proteins. On the basis of the developed approach, a qualitative correlation of the obtained results with the dissociation constant was revealed using the example of the forma...

In this chapter, two algorithms have been developed, one of which (Algorithm 3) was developed specifically for the selection of amino acid residues in peptides to improve their affinity in the interaction of peptides with full-length proteins, and Algorithm 4 was developed to search for “scattered” active region of the protein when bound to the pep...

This chapter we construct a physical model of the interactions between protein molecules and study of their propensity to form biological complexes. The reactivities of proteins have been studied using electrostatics methods based on the example of histones H2A, H2B, H3, H4. The capability of proteins to form stable biological complexes that allow...

This chapter discusses various experimental approaches for determining the structure of molecules, the mutual arrangement of domains in space, the identification of active protein centers, and their advantages and limitations in the study of various physical properties of biological complexes.

This chapter presents a physical model of phosphorylation the amino acid residues of the polypeptide chain of a protein on the formation of biological complexes with other proteins.

We report on the results of mathematical simulation of the interaction of various sequences of proteins Mdm2, P53, and Nap1 in accordance with the developed algorithms that were used for identifying the region of binding of various proteins during the formation of biological complexes P53–Mdm2, Mdm2–Mdm2, and Nap1–Nap1. The approach developed in th...

A new method enabling the qualitative determination of the dissociation constant of peptides to full-length proteins and the estimation of the effect of point mutations in peptides on the stability of a formed complex with whole proteins was presented. Based on the developed approach, a qualitative correlation was revealed between the obtained resu...

The mathematical model is proposed for determination of the optical parameters on the basis of spectrophotometric data.

We study optical characteristics of an ensemble of arbitrarily oriented particles are studied in an optical cavity. The study is based on the self-consistent conjugation with respect to nonuniform optical cavities with the results of scattering by an ensemble of arbitrarily oriented spherical particles with different shapes and structures. A new el...

We construct the mathematical model for calculating the interaction of laser radiation with a turbid medium and the model for the prediction of the optical characteristics of blood (refractive index and absorption coefficient) and for the determination of the rate of blood flow in the capillary bed under irradiation of a laser beam is proposed.

The mathematical model proposed for detection the the function of size distribution of form for blood cells. Using the mathematical model we can theoretically calculate the size distribution function for particles of irregular shape with a variety forms and structures of inclusions that simulate blood cells in the case of in vivo and determine the...

We construct the electrodynamic model which makes it possible to vary the electrophysical parameters of a biological structure in calculations with allowance for roughness (real and imaginary parts of the refractive index of the epidermis, the upper layer of the derma, and blood) and to establish the dependences between these parameters and the bio...

We propose the mathematical model for calculation of the hyperthymia of a multilayer biological structure under the action of laser radiation. For the case in vivo, the dependences of the temperature field on the refractive index and absorption coefficient of the biological tissue under study (epidermis, the upper derma layer, the lower derma layer...

We describe the mathematical model, which allows us to vary the electrical parameters and structure of the simulated biological tissue with fibrillar structure for case in vivo.

The mathematical model proposed for predicting optical characteristics (refractive index and absorption coefficient) of a biotissue being simulated, which is probed in vivo by a laser beam. Blood corpuscles in this case are simulated by particles of irregular shape and various sizes, which are oriented arbitrarily in free space. Using the mathemati...

We construct the mathematical model, which makes it possible to vary the characteristic sizes of roughness, the electrophysical parameters of the biological sample under investigation, and its geometrical characteristics and to establish the relations between these parameters and biological properties of the biological tissue being modeled, as well...

We consider the structure and optical properties of biological tissues, blood and thermophysical characteristics of the elements in the skin tissue.

We propose methods of light scattering for the quantitative study of the optical characteristics of the tissue, and the results of theoretical and experimental studies of photon transport in biological tissues.

We describe a mathematic model for predicting the absorption spectrum and dispersion of a section of a biological structure consisting of epidermis, upper layer of the derma, blood, and lower layer of the derma and placed in the cavity of an optical resonator. It should be noted that the biological structure was represented by layers with different...

This work is devoted to the mathematical modeling of the temperature effect on the stability of H2A–H2B and Н3–H4 histone dimers by studying their behavior in different temperature regimes of 20–50°C. The study of the thermal stability of these two dimers in aqueous solutions at different temperatures has revealed their multifarious behavior at tem...

A physical model of the interaction of protein molecules and their ability to form complex biological systems for the in vitro case in a solution of monovalent salt has been developed. Their reactive abilities using the methods of electrostatics based on the example of the step-by-step formation of the histone octamer from the H2A, H2B, H3, and H4...

A physical model of the interactions between protein molecules has been presented and an analysis of their propensity to form complex biological complexes has been performed. The reactivities of proteins have been studied using electrostatics methods based on the example of the histone chaperone Nap1 and histones H2A and H2B. The capability of prot...

A physical model of interactions of protein molecules has been developed. The regularities of their reactivity have been studied using electrostatics methods for two histone dimers H2A–H2B and H3–H4 assembled from monomers. The formation of histone dimers from different monomers has been simulated and their ability to the formation of stable compou...

Size distribution functions of colloid particles are obtained with the aid of dynamic light scattering for both polarized and depolarized components. Electron microscopy of the colloid particles is used to construct size distribution histograms. Numerical analysis yields good agreement of the experimental and theoretical size distributions. The siz...