Deep learning and machine learning models
Artificial intelligence in pharmaceutical and biochemical preliminary research
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Obtaining preliminary research data for biological systems: protein-protein interactions, missense mutations
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Saving financial resources in experimental biochemical research
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List of free software, machine learning software, paid software. How to get software for personal PC and corporate use.
I am interested in examples of completed research. I want to see correlation dependencies between calculated and experimental calculations:
Get preliminary results. See the full list of practical calculations performed using AI and deep learning.
a) Separation of mutations into oncogenic and non-oncogenic using calculated physical data obtained by deep learning methods
b) Correlation plots between experimental and calculated data for denatured proteins in a denaturant solution
c) Calculation of physical properties for proteins in salt solutions
d) Why are we investigating electrostatic interactions?
- we are often asked about this, because "there are many other interactions."
I am interested in using an online server for biochemical calculations
Check out the full range of online calculations performed for proteins, peptides, dimers, tetramers, inhibitors. Perform the calculation yourself by uploading the source data and get a data file.
Watch training videos
There are many different videos on science, on the topic of research, calculations of affinity and charges of small molecules are presented here
Get acquainted with the mathematical part, see the section on quantum mechanics. See the mathematical part pdf files
I would like to watch math problems, math formula
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In connection with the many meetings and negotiations held with startups, business angels, managers, investors, it was decided to simplify the presentation of material to clear visual presentations with colorful design.
It is also always worth remembering that the key to successful work
this is a well-coordinated teamwork to obtain a quality result.
It is also always worth remembering that the key to successful work
this is a well-coordinated teamwork to obtain a quality result.
Tatiana Koshlan
Biochemical | Biological Sciences
Software for biotech companies
that allow you to recieve preliminary results
before conducting a laboratory experiment
for biological molecules
that allow you to recieve preliminary results
before conducting a laboratory experiment
for biological molecules
Monoclonal antibody
Online Server for selection of flexible antibody chains to antigen, target protein, using deep learning method. Using unique software
Viral Proteins
Determination of the direction of affinity change upon replacement of key amino acid residues
Small molecules
Determination of Suitable Small Molecules for Cancer Changes in Proteins
Amyloid peptides
Selection of peptide sequences to increase the stability of amyloid complexes
Our research can be divided into fundamental (basic) and applied biological researches.
Our research can be divided into fundamental (basic) and applied biological researches.
Molecular biophysics is the study of the physical principles governing biomolecular systems. It seeks to explain biological function in terms of molecular structure, dynamics and organization, from single molecules to supramolecular structures.
Short Examples
DIRECTION OF AFFINITY CHANGE
comparison of experimental (Kd, IC50) and calculated values (lg(cond(W)), deltaH)
DIRECTION OF AFFINITY CHANGE
comparison of experimental (Kd, IC50) and calculated values (lg(cond(W)), deltaH)
1
Using Machine Learning and AI to Generate Preliminary Results for Identifying Missense Mutations Involved in Drug Resistance
Erlotinib-EGFR
Erlotinib is used to treat certain types of non-small cell lung cancer that has spread to nearby tissues or to other parts of the body in patients who have already been treated with at least one other chemotherapy medication and have not gotten better. A value lg(cond(W)) that shows the stability of a biological complex and shows the direction of change in the affinity of a dimer under various mutations. The results of applying our technique can be of good help for the pre-experimental determination of such quantities as the affinity expressed by the dissociation constant or the half maximal inhibitory concentration (IC50).
THE FIRST GRAPH (RED) SHOWS THE DEPENDENCE OF THE VALUE IC50 ON THE MUTATION IN THE EGFR PROTEIN, THE SECOND GRAPH (BLUE) SHOWS THE RESULTS OF THE CALCULATIONS USING THE SOFTWARE DEVELOPED BY US, WHICH SHOWS THE DIRECTION OF THE CHANGE IN AFFINITY FOR MUTATIONS IN PROTEINS
The experimental values were taken [In vitro modeling to determine mutation specificity of EGFR tyrosine kinase inhibitors against clinically relevant EGFR mutants in non-small-cell lung cancer]
1. Thus, the numerical method developed by us makes it possible to determine the range of changes in the stability of dimeric complexes with the participation of a small chemical molecule and a protein molecule.
2. Application of our method will allow us to identify mutations that lead to a decrease in the affinity of components.
3. Numerical analysis requires a three-dimensional structure of the dimer under study, in the protein component of which substitutions of amino acid residues will be introduced.
2
Imatinib-PPAR
Imatinib is used to treat certain types of leukemia (cancer that begins in the white blood cells) and other cancers and disorders of the blood cells. Imatinib is also used to treat certain types of gastrointestinal stromal tumors.
Peroxisome proliferator-activated receptor (PPAR ) belongs to the thyroid hormone receptor-like nuclear receptor subfamily 1, which is one of the ligand-activated transcription factors.
Chemical structure of Imatinib-PPAR dimer with indication of key amino acid residues.
Useful application of the obtained numerical results.
The results of our studies can be applied in predicting:
- Inhibitory potency and binding ability of small molecules
- Inhibitor dissociation constants for the WT and mutant
kinases
- Enzyme kinetic parameters
- Explain the enhanced drug sensitivity of different mutants
- Changing in the binding site caused by
the mutation on the enzyme's binding affinity for TKIs
- Enzyme kinetic assays and IC50 determinations
- Inhibitor binding constants, the drug resistance
3
Naquotinib (ASP8273)-EGFR
Naquotinib (ASP8273) 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 mutations. Naquotinib is an orally available, irreversible, third-generation, mutant-selective, epidermal growth factor receptor (EGFR) inhibitor, with potential antineoplastic activity. Upon oral administration, ASP8273 covalently binds to and inhibits the activity of mutant forms of EGFR, including the T790M EGFR mutant, thereby preventing EGFR-mediated signaling. ASP8273 preferentially inhibits mutated forms of EGFR including T790M, a secondarily acquired resistance mutation, and may have therapeutic benefits in tumors with T790M-mediated resistance when compared to other EGFR tyrosine kinase inhibitors. As this agent is selective towards mutant forms of EGFR, its toxicity profile may be reduced as compared to non-selective EGFR inhibitors which also inhibit wild-type EGFR.
Naquotinib (ASP8273) 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 mutations. Naquotinib is an orally available, irreversible, third-generation, mutant-selective, epidermal growth factor receptor (EGFR) inhibitor, with potential antineoplastic activity. Upon oral administration, ASP8273 covalently binds to and inhibits the activity of mutant forms of EGFR, including the T790M EGFR mutant, thereby preventing EGFR-mediated signaling. ASP8273 preferentially inhibits mutated forms of EGFR including T790M, a secondarily acquired resistance mutation, and may have therapeutic benefits in tumors with T790M-mediated resistance when compared to other EGFR tyrosine kinase inhibitors. As this agent is selective towards mutant forms of EGFR, its toxicity profile may be reduced as compared to non-selective EGFR inhibitors which also inhibit wild-type EGFR.
4
Rociletinib (CO-1686)-EGFR
Rociletinib (CO-1686) is an irreversible, mutant-selective EGFR inhibitor. It is a medication developed to treat non-small cell lung carcinomas with a specific mutation. It is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor. It was being developed by Clovis Oncology as a potential treatment for non-small-cell lung cancer.
A value lg(cond(W)) that shows the stability of a biological complex and shows the direction of change in the affinity of a dimer under various mutations.
Software Data Results
The results of numerical calculations of two different structures (5XDK and 5XDL) EGFR-Rociletinib (CO-1686) are in good agreement.
1. Substitution of L844V leads to a decrease in the stability of the mEGFR (L844V) - Rociletinib dimeric complex when analyzing the 5XDK and 5XDL sutures (the difference in the cond (W) value between the two mEGFR (L844V) - Rociletinib and wtEGFR-Rociletinib complexes was 300)
2. Replacement of T790M leads to increased resistance of mEGFR (T790M) - Rociletinib
3. Double substitution of T790M / L858R leads to a significant increase in the stability of the mEGFR dimer (T790M / L858R) - Rociletinib. Numerical calculations of the two structures showed similar results.
4. Replacement of L858R led to an increase in the stability of the mEGFR complex (L858R) - Rociletinib
Thus, the numerical method developed by us makes it possible to determine the range of changes in the stability of dimeric complexes with the participation of a small chemical molecule and a protein molecule. Application of our method will allow you to identify mutations that lead to a decrease in the affinity of components. Numerical analysis requires a three-dimensional structure of the dimer under study, in the protein component of which substitutions of amino acid residues will be introduced.
The results of numerical calculations of two different structures (5XDK and 5XDL) EGFR-Rociletinib (CO-1686) are in good agreement.
1. Substitution of L844V leads to a decrease in the stability of the mEGFR (L844V) - Rociletinib dimeric complex when analyzing the 5XDK and 5XDL sutures (the difference in the cond (W) value between the two mEGFR (L844V) - Rociletinib and wtEGFR-Rociletinib complexes was 300)
2. Replacement of T790M leads to increased resistance of mEGFR (T790M) - Rociletinib
3. Double substitution of T790M / L858R leads to a significant increase in the stability of the mEGFR dimer (T790M / L858R) - Rociletinib. Numerical calculations of the two structures showed similar results.
4. Replacement of L858R led to an increase in the stability of the mEGFR complex (L858R) - Rociletinib
Thus, the numerical method developed by us makes it possible to determine the range of changes in the stability of dimeric complexes with the participation of a small chemical molecule and a protein molecule. Application of our method will allow you to identify mutations that lead to a decrease in the affinity of components. Numerical analysis requires a three-dimensional structure of the dimer under study, in the protein component of which substitutions of amino acid residues will be introduced.
5
The influence of missense mutations on the physical properties of molecular interactions. Correlation analysis between calculated and experimental data.
Mcl1-Bax BH3
Myeloid leukemia 1 (MCL-1) is an antiapoptotic protein of the BCL-2 family that prevents apoptosis by binding to the pro-apoptotic BCL-2 proteins. Overexpression of MCL-1 is frequently observed in many tumor types and is closely associated with tumorigenesis, poor prognosis and drug resistance. The central role of MCL-1 in regulating the mitochondrial apoptotic pathway makes it an attractive target for cancer therapy. Various Bax Met-74 mutants disrupt interactions between Bax and all pro-survival proteins, but these Bax mutants retain pro-apoptotic activity.
ANALYSIS OF BINDING OF BAX MET-74 MUTANT PEPTIDES TO PRO-SURVIVAL PROTEINS USING A BIACORE-BASED COMPETITION ASSAY VALUES ARE PRESENTED AS AN IC50 IN NM, AND VALUES IN BRACKETS REPRESENTS S.D.
(N =2–3 ASSAYS).
Comparing graphs a) and c), we see that the maximum value of IC50 and lg (cond (W)) falls on the replacement 74Asp. Thus, the replacement of methionine at position 74 of the Bax protein in the BH3 domain with Asp leads to the maximum decrease in resistance according to theoretical calculations and to the maximum loss of mutant peptide binding to Mcl1 protein. Thus, the maximum decrease in the stability of the Bax Bh3 (MET74ASP) -Mcl1 dimer corresponds to a significant loss of the peptide's ability to bind to the protein, according to the experimental data.
Since the first 4 results are graphically in the same range (at the bottom of the experimental and theoretical plots) compared to the maximum value of 74Asp, we decided to separately present these 4 values in plots b) and d) with an indication of the experimental error. According to the obtained theoretical and experimental data, the most stable is the wild-type wtBax BH3-Mcl1 dimer, while the wild-type Bax BH3 peptide has the greatest ability to bind to the Mcl1 protein compared to all the presented substitutions of amino acid residues in the Bax BH3 peptide.
6
Selection of flexible antibody-to-antigen chains using deep learning method.
Antibody-Antigen. Fab-CD20
Rituximab is a chimeric monoclonal antibody to the CD20 transmembrane antigen, expressed on the surface of B-lymphocytes and regulating lymphoid cell differentiation from an immature lymphocyte to a plasma cell. After rituximab binds to the CD20 antigen, a multi-stage complement system is activated on the surface of the B-lymphocyte, with the last stage being the formation of the C9 protein.The main innovation for the method proposed in this article is the determination of changes in the stability of the tetrameric complex, as well as the development of an original technique and the corresponding software package. These would allow researchers to determine the range of changes in the affinity of a biological complex when replacing amino acid residues in polypeptide chains; in this case, an antibody or antigen. We adapted the original method that we developed, in order to examine tetrameric antibody-antigen complexes. For this
purpose, we used a ready-made three-dimensional structure, which is a biological comprising six units, as presented in the PDB database: 6VJA
Antibody-Antigen. Fab-CD20
Rituximab is a chimeric monoclonal antibody to the CD20 transmembrane antigen, expressed on the surface of B-lymphocytes and regulating lymphoid cell differentiation from an immature lymphocyte to a plasma cell. After rituximab binds to the CD20 antigen, a multi-stage complement system is activated on the surface of the B-lymphocyte, with the last stage being the formation of the C9 protein.The main innovation for the method proposed in this article is the determination of changes in the stability of the tetrameric complex, as well as the development of an original technique and the corresponding software package. These would allow researchers to determine the range of changes in the affinity of a biological complex when replacing amino acid residues in polypeptide chains; in this case, an antibody or antigen. We adapted the original method that we developed, in order to examine tetrameric antibody-antigen complexes. For this
purpose, we used a ready-made three-dimensional structure, which is a biological comprising six units, as presented in the PDB database: 6VJA
The three-dimensional structure and matrix of tetramer
Antibody affinity describes the intensity with which a single antibody molecule binds to its specific epitope in an antigen. This means that under a given concentration of antibody and
antigen, a specific number of antigen-antibody complexes are formed. Consequently, antibody affinity is one of the major properties affecting the potency of therapeutic antibodies. Binders with higher affinities may allow for lower doses or longer intervals of administration during therapy. Moreover, as antibodies require sophisticated production systems and therapeutic doses, and costs of goods of antibodies are comparably high, a high affinity may affect the commercial success of a therapeutic antibody. The process of in vivo affinity maturation is described as well as strategies for in vitro affinity maturation. Finally, the relation between affinity and efficacy and the determination of antibody affinity are reviewed. The correct determination of antibody affinity is crucial for antibody development, as wrongly set up experiments may result in the further development of the wrong candidate antibody. This can result in low in vivo efficacy, especially when high-affinity antibodies are needed; for example, for neutralizing antibodies.
Thus, there is no need to conduct expensive preliminary experiments to test different antibody modifications with our developed software package. We now have a unique opportunity to
use our developed software to determine the affinity of the antibody-antigen complex and its various modifications in the case of missense mutations.
antigen, a specific number of antigen-antibody complexes are formed. Consequently, antibody affinity is one of the major properties affecting the potency of therapeutic antibodies. Binders with higher affinities may allow for lower doses or longer intervals of administration during therapy. Moreover, as antibodies require sophisticated production systems and therapeutic doses, and costs of goods of antibodies are comparably high, a high affinity may affect the commercial success of a therapeutic antibody. The process of in vivo affinity maturation is described as well as strategies for in vitro affinity maturation. Finally, the relation between affinity and efficacy and the determination of antibody affinity are reviewed. The correct determination of antibody affinity is crucial for antibody development, as wrongly set up experiments may result in the further development of the wrong candidate antibody. This can result in low in vivo efficacy, especially when high-affinity antibodies are needed; for example, for neutralizing antibodies.
Thus, there is no need to conduct expensive preliminary experiments to test different antibody modifications with our developed software package. We now have a unique opportunity to
use our developed software to determine the affinity of the antibody-antigen complex and its various modifications in the case of missense mutations.
«
An additional example applications of the developed method
Startup pitch decks of high lifescience innovations.
The main goal
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:
the mutation on the enzyme's binding affinity for TKIs
UP TITLE
Thanks to the use of the software developed by us,
you can determine the affinity range of the biological complex
before carry out the biological experiment.
you can determine the affinity range of the biological complex
before carry out the biological experiment.
Why choose us?
Our software allows you to determine the direction of affinity change, so you can significantly save on the following experimental methods:
- ELISAs
- Gel-shift assays
- Aanalytical ultracentrifugation
- Surface plasmon resonance
- Spectroscopic assays
- Affinity electrophoresis
- Isothermal Calorimetry
FAQ.
Why are we investigating electrostatic interactions?
Why are we investigating electrostatic interactions?
- we are often asked about this, because "there are many other interactions."
This part is devoted to a frequently asked question regarding electrostatic interactions, which are the main ones in our research.
Solvation (from lat. Solvo "dissolve") - electrostatic interaction between particles (ions, molecules) of a dissolved substance and a solvent. Solvation in aqueous solutions is called hydration. The molecular aggregates formed as a result of solvation are called solvates (in the case of water, hydrates)
Van der Waals forces (Van der Waals forces) are the forces of intermolecular (and interatomic) interaction with an energy of 10–20 kJ / mol. This term originally denoted all such forces, in modern science it is usually applied to the forces arising from the polarization of molecules and the formation of dipoles.
Classification of van der Waals forces:
The van der Waals interaction consists of three types of weak electromagnetic interactions:
Orientation forces, dipole-dipole attraction. It is carried out between molecules that are permanent dipoles. An example is HCl in liquid and solid state. The energy of this interaction is inversely proportional to the cube of the distance between the dipoles.
Dispersive attraction (London forces, dispersion forces). They are due to the interaction between the instantaneous and the induced dipole. The energy of this interaction is inversely proportional to the sixth power of the distance between the dipoles.
Induction attraction (polarization attraction). Interaction between permanent dipole and induced (induced). The energy of this interaction is inversely proportional to the sixth power of the distance between the dipoles.
The dipole moment is an important molecular constant that characterizes the electrical symmetry of a molecule. Knowledge of the magnitude of the dipole moment is necessary for studying the nature of chemical bonds, assessing the strength of donor-acceptor and intermolecular bonds, for quantum-chemical calculations.
Electric dipole moment is a vector physical quantity that characterizes, along with the total charge (and rarely used higher multipole moments), the electrical properties of a system of charged particles (charge distribution) in the sense of the field they create and the action of external fields on it. After the total charge and the position of the system as a whole (its radius vector), the main characteristic of the configuration of the charges of the system when observing it was published
Dispersion forces (dispersive attraction, London forces, London dispersion forces, LDF) are the forces of electrostatic attraction of instantaneous and induced (induced) dipoles of electrically neutral atoms or molecules.
A hydrogen bond is a form of association between an electronegative atom and a hydrogen atom H, covalently bonded to another electronegative atom. N, O, or F can act as electronegative atoms. Hydrogen bonds can be intermolecular or intramolecular
Donor-acceptor interaction - charge transfer between donor and acceptor molecules without the formation of a chemical bond between them (exchange mechanism); or the transfer of a lone electron pair from a donor to an acceptor, leading to the formation of a bond (donor-acceptor mechanism).
Introductory video on the practical use of our software
Using our software package you can determine the range of changes in affinity and then select only those modifications for further experimental research that meet the set objectives, for example, antibody modifications that will increase the affinity to the antigen, but will not lead to aggregation of antibodies among themselves.
Description of the software package for determining the stability of protein molecules.
free video editing software,toolbox medical innovations
TUTORIAL BIOLOGICAL SOFT. The figures show two graphs showing the results of the effect of mutations in the BAK peptide on binding to the Bcl-xl protein. The graph on the left is from an experimental study.
The figure shows a tetramer consisting of two CD20 transmembrane proteins and two FABs, heavy and light chains We will introduce five mutations in turn into the active binding site with CD20 and analyze the change in stability.
The purpose of this project is to develop a method (biological software)that allows one to determine the effect of mutations from the known structure of a biological molecule on the binding affinity
Molecular Therapies of Cancer
Our team has developed an innovative method for determining the stability of chemical compounds, taking into account various oncogenic mutations. Useful application of the obtained numerical results
Gefitinibe
Gefitinib inhibits the catalytic activity of numerous tyrosine kinases including the epidermal growth factor receptor (EGFR), which may result in inhibition of tyrosine kinase-dependent tumor growth. Specifically, this agent competes with the binding of ATP to the tyrosine kinase domain of EGFR, thereby inhibiting receptor autophosphorylation and resulting in inhibition of signal transduction.
AMP
The T790M mutation of EGFR increases the ATP affinity of the G719S mutant, explaining the acquired drug resistance of the double mutant. Structural analyses of the G719S/T790M double mutant, as well as the wild type and the G719S and L858R mutants, revealed that the T790M mutation stabilizes the hydrophobic spine of the active EGFR-TK conformation.
CO-1686
Rociletinib (CO-1686) is an irreversible, mutant-selective EGFR inhibitor. It is a medication developed to treat non-small cell lung carcinomas with a specific mutation. It is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor. It was being developed by Clovis Oncology as a potential treatment for non-small-cell lung cancer
Imatinib
Imatinib is specific tyrosine kinase receptor inhibitor that is used in the therapy of Philadelphia chromosome-positive chronic myelogenous leukemia and gastrointestinal stromal tumors, both of which are marked by an abnormal, constitutively expressed tyrosine kinase that causes unregulated cell growth.
Now let's analyze, and then perform example of replacing an amino acid residue in a Bak peptide when it interacts with the whole protein Bcl xl, which leads to an increase in the affinity of the peptide to the protein. Let us consider in more detail the three-dimensional structure of this dimer. Initially, we have a 3D structure of a dimer, in which the Q77L substitution in the Bak peptide is performed. The overall structure of BAKQ77L was not significantly affected by the mutation, and the side chain of L77 is oriented identically to the wild-type glutamine at this position on the solvent-exposed surface of the (BH3) helix.
Example 2: guide to biological software
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Antibody Affinity
Biophysics of the affinity of the antibody-antigen biocomplex
Our group developed an innovative method in biology for antibody-antigen development. You don't have to spend money to carry out the experiment.
The correct determination of antibody affinity is crucial for antibody development as a wrong setup of the experiments may result in the further development of the wrong candidate antibody. This can result in low in vivo efficacy, especially when high-affinity antibodies are needed, for example, for neutralizing antibodies.
Our group has developed an innovative research technique for such a complex using Data Science
Our group has developed an innovative research technique for such a complex using Data Science
Learn More
Coronavirus (Covid-19) is a world pandemic. A step-by-step guide to the analysis of affinity of interaction by Soft using
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 interaction by comparing 3 criteria, presents an analysis of energy interactions between the active center of a protein and the wild-type peptide interacting with it and taking into account modifications of the latter.
Learn More
New Approaches for Aggregation Mechanisms in Amyloids
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 other amyloid peptides to achieve equilibrium.
It remained to solve the question: how will we determine the stability of the dimeric complex
It remained to solve the question: how will we determine the stability of the dimeric complex
Learn More
DATABASE OF TARGETED ANTITUMOR THERAPY FOR EGFR PROTEINS: HER2 AND HER3. Soft application.
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-small cell lung cancer. Most people have relatives or friends who are sick or who have already left us. In 2017, 9.6 million people are estimated to have died from the various forms of cancer. Every sixth death in the world is due to cancer, making it the second leading cause of death — second only to cardiovascular diseases.
What is hydrophobic interaction?
The most common explanation is that hydrophobic molecules "do not like" to interact with the aqueous environment. We obtained the values of hydrophobic interactions, calculated their value, developed a method for determining the range of interactions, and developed a graphical representation using soft, math, data science. You can free download soft and learn Data Scince
hydrophobic interactions
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Additional information
Protein-protein interactions. Miscellaneous.
Examples of various calculations taking into account three-dimensional structure, as well as without taking into account three-dimensional structure
P73-P73
3D Maps
p73 is a structural and functional homologue of the p53 tumor suppressor protein. Like p53, p73 induces apoptosis and cell cycle arrest and transactivates p53-responsive genes, conferring its tumor suppressive activity. In addition, p73 has unique roles in neuronal development and differentiation.
p73 is a structural and functional homologue of the p53 tumor suppressor protein. Like p53, p73 induces apoptosis and cell cycle arrest and transactivates p53-responsive genes, conferring its tumor suppressive activity. In addition, p73 has unique roles in neuronal development and differentiation.
P53-P53, P63-P63, P73-P73 protein interactions
Linear Docking. Bellow we present the results of mathematical simulation of the interaction of various sequences of proteins p53, p63, and p73 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-p53, p63-p63, and p73-p73.
Nap1-Nap1 interactions (3D Map)
A new method, which analyzes the potential energy of electrostatic interaction of protein complexes at point replacements of amino acid residues assuming a three-dimensional structure of the complex on the example of formation of a Nap1–Nap1 dimer, has been presented. Maps of potential energy of electrostatic interaction of paired amino acid residues of participating proteins have been developed.
Nap1-Nap1, Mdm2-Mdm2
Linear Docking. Bellow we present 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.
Behind the big data
Fundamental (basic) research
Mathematical [math] methods, soft, data science and their physical application
Advance techniques and Physical Applications provides a wide range of basic math concepts and methods, which are relevant to biophysic theory and biomolecule. This page is devoted to the physical and mathematical modeling of the formation of complexes of protein molecules, antibody and amyloid peptide (alzheimer desease). Real techniques show remarkable sensitivity to the amino acid sequences of proteins, which facilitates experimental studies in lab and allows one to reduce the associated costs by reducing the number of measurements required according to the developed criteria in experimental lab. These models make it possible to reach a conclusion about the interactions between different amino acid chains and to identify more stable sites on proteins via control techniques, soft and Data Science. The models also take the phosphorylation of amino acid residues into account.
You can download soft for antibody cost saving and learn Data Scince
You can download soft for antibody cost saving and learn Data Scince
Interaction of hydrophobic molecules
It became possible to quantify the hydrophobic effect using data science, soft and biophisical methods: calculate the magnitude and value of the potential energy of pairwise electrostatic interactions between each pair of hydrophobic amino acid residues of two protein.
CALCULATION OF ENTROPY CHANGE
For obtain a numerical estimate of this interaction we estimate the change differential entropy for one-dimensional and multidimensional case using software, data scince and math.
Kogbetliantz's algorithm
Kogbetliantz's algorithm for the singular-value decomposition (SVD) of an arbitrary matrix can be viewed as a natural extension of Jacobi's method for the eigenvalue decomposition of a symmetric, Hermitian, or normal matrix.
Singular Value Decomposition
In linear algebra, the Singular Value
Decomposition (SVD) of a matrix is a factorization of that matrix
into three matrices.You can use this technique and also learning data science
Decomposition (SVD) of a matrix is a factorization of that matrix
into three matrices.You can use this technique and also learning data science
Debye length
The Debye length (also called Debye radius), named after Peter Debye, is a measure of a charge carrier's net electrostatic effect in a solution and how far its electrostatic effect persists.
The Gouy–Chapman theory
The Gouy-Chapman theory describes a rigid charged surface, with a cloud of oppositely charged ions in the solution, the concentration of the oppositely charged ions decreasing with distance from the surface. This is the so-called diffuse double layer.
Algorithm rotation
This algorithm, taking into account the rotation of one amino acid
residue allows you to find the stability of protein-protein complexes, peptide-peptide complex, peptide-protein complex with a
known amino acid sequence and with the known three-dimensional structure from X-ray analysis.
residue allows you to find the stability of protein-protein complexes, peptide-peptide complex, peptide-protein complex with a
known amino acid sequence and with the known three-dimensional structure from X-ray analysis.
Static algorithm
An algorithm and software package was developed for analyzing protein interactions, taking into account their three-dimensional
structure from the PDB database.
structure from the PDB database.
Mathematical modelling of the effect of phosphorylation of biological complexes
A physical and mathematical model was developed to take into account the phosphorylation effect
What researches are you interested in?
Here you can ask a question, talk about the goals of your research.
