OUR COMPANY
Linear Protein Docking
The correlations were performed on real solutions in a biochemical laboratory.
Development of a unique platform for automated search for interaction sites
We present the developed algorithm for a step-by-step transparent and understandable
search for interaction areas, each of which will be characterized by numerical physical
quantities.
Cost AI calculations for linear sequences:
Use the linear docking method, which allows you to determine the most stable binding regions according to the amino acid sequence. We propose to carry out the check with entire domains, i.e. to divide the molecule into structural elements, to determine the most contact amino acid sequences by the method of linear docking.
The interaction between sites will be characterized by numerical indicators, which will allow for a visual gradation.
The interaction between sites will be characterized by numerical indicators, which will allow for a visual gradation.
Use the linear docking method developed by us, which allows us to determine the most stable binding regions according to the amino acid sequence
We propose to carry out the check with entire domains, i.e. to divide the molecule into structural elements, to determine the most contact amino acid sequences by the method of linear docking.
The interaction between sites will be characterized by numerical indicators, which will allow for a visual gradation.
We propose to carry out the check with entire domains, i.e. to divide the molecule into structural elements, to determine the most contact amino acid sequences by the method of linear docking.
The interaction between sites will be characterized by numerical indicators, which will allow for a visual gradation.
Parsing the structure into domains:
1) alpha spirals, beta sheets, turns
2) intramolecular bonds that provide the formation of domains
3) Conducting calculations on domain interactions
Checking the correctness of the 3D model based on the available data
1) obtaining the physical characteristics of interacting molecules:
1) alpha spirals, beta sheets, turns
2) intramolecular bonds that provide the formation of domains
3) Conducting calculations on domain interactions
Checking the correctness of the 3D model based on the available data
1) obtaining the physical characteristics of interacting molecules:
- stability,
- entropy change,
- Gibbs energy,
- Constant dissociation,
- Enthalpy change,
- The thermal dissociation,
- Potential energy of electrostatic interaction between all amino acid residues taken in pairs
a) MYC domain structure
Top: MYC protein is shown with conserved MYC boxes (MB) highlighted in red colours. Numbers
below indicate amino acids of human c-MYC. MB0, which is located N-terminally of MBI, is not
annotated.
Below: three protein structures have been resolved in
complex with MYC, namely AURKA, WDR5, and MAX.
[ MYC shapes the composition of RNA
polymerase II through direct recruitment of transcription elongation factors]
b) Organization of the main protein domains and conservation across different MYC super-family
members.
[Therapeutic targeting of “undruggable” MYC]
c) Schematic of WWP1, WWp2 and ITCH domains showing an enzymatic activity summary derived
from the autoubiquitination assay.
[A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases]
Top: MYC protein is shown with conserved MYC boxes (MB) highlighted in red colours. Numbers
below indicate amino acids of human c-MYC. MB0, which is located N-terminally of MBI, is not
annotated.
Below: three protein structures have been resolved in
complex with MYC, namely AURKA, WDR5, and MAX.
[ MYC shapes the composition of RNA
polymerase II through direct recruitment of transcription elongation factors]
b) Organization of the main protein domains and conservation across different MYC super-family
members.
[Therapeutic targeting of “undruggable” MYC]
c) Schematic of WWP1, WWp2 and ITCH domains showing an enzymatic activity summary derived
from the autoubiquitination assay.
[A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases]
Features of the interaction of Aurora-A kinase domains and N-MYC peptide, with an indication of the numerical value.
Let's move on to the analysis of spatial interactions between the found domains.
Identification of the most significant interactions (with the least number of conditions) between domains
The colors represent the interaction areas found for the linear model and transferred to the spatial model.
TP53=MEESQSELNIDPPLSQETFSELWNLLPENNVLSSELCPAVDELLLPESVVNWLDEDSDDAPRMPATSAPTAPGPAPSWPLSSSVPSPKTYPGTYGFRLGFLHSGTAKSVT
Cost AI calculations for linear sequences:
We will be happy to accept your financial assistance and donations!
Thank you very much for your interest in our work, it motivates us to continue working and to carry out both academic research and practical software developments dedicated to accelerating preclinical and clinical research in medicine.
If you are ready to support us financially, then for your convenience we have implemented DonorBox on the page of our website for promotional donation on your part, as well as for payment of settlement services
Basic needs:
Payment of software development specialists, security, payment for academic research,
purchase of equipment, depreciation of existing equipment, rent, taxes, transportation costs,
food, baking, coffee for employees
If you are ready to support us financially, then for your convenience we have implemented DonorBox on the page of our website for promotional donation on your part, as well as for payment of settlement services
Basic needs:
Payment of software development specialists, security, payment for academic research,
purchase of equipment, depreciation of existing equipment, rent, taxes, transportation costs,
food, baking, coffee for employees
