A deep learning method for predicting antibody-antigen interactions based on sequence information
Antibody Sequencing Service Data platform for Antibody-Antigen calculations: Antigen-Fab-Fab
Algorithm 20
How Antibody Sequencing Works
Starting with just 50μg of purified antibody, the sample undergoes multi-enzyme digestions. The fragments are measured with LC-MS/MS for de novo sequencing of the peptides. These peptides are analyzed by Rapid Novor’s suite of bioinformatics algorithms to assemble the full-length heavy and light chain antibody sequences. Monoclonal antibody sequencing works on any species and isotype.
Experimental hard wocking
Point mutations by somatic hypermutation increase variation into the variable region and occur a million-fold more frequently than other genetic mutations.
Somatic Hypermutation
SHM facilitates the progressive increase in antibody affinity against the antigen known as affinity maturation (Figure 4). Some immunoglobulin mutants bind antigens better than others, while some mutants produce non-productive rearrangements. Mutations in the framework regions of the variable domain tend to be selected against as they don’t enhance antigen-binding and alter the basic antibody structure. Mutations that enhance antigen-binding tend to be clustered in the CDR regions.
Strong-affinity binders are selected for and proliferate and mature into antibody-secreting cells, whereas lower affinity clones are eliminated by apoptosis.
Affinity maturation increases antibody activity through multiple rounds of somatic hypermutation and selection in the germinal center.
Experimental hard wocking
Experimental Cost of Antibody Development
Use AI and Machine Learning Methods for
Hyper Mutation Analysis of Flexible Antibody Chains to Increase Affinity of Antibody to Antigen (Epitope)
The structure of a typical antibody molecule
Below are the recommended schemes of the biological complex that speed up the operation of the calculation server.
Preparation of Antibodies for calculations. Large Antibody structures will be automatically moved to the end of the queue.
Preparation of the calculation complex as a whole:
Obtain a complete set of physical interaction parameters for Antigen-Fab2that have contact through interacting domains.
An example of the PDB structure is given below on the page.
An example of the obtained calculated data, correlation with experiment and the use of machine learning methods, see below on the page.
You can introduce mutations into one PDB at once, up to 4 mutations at the same time. It is desirable that the mutations do not occur one after another, but are spaced and separated by other amino acid residues. The server does not SEARCH FOR THE CONTACT AREA; it is assumed that the structure's PDB already contains this spatial information.
To obtain more accurate results, it is necessary to separately analyze mutations in the heavy chain from mutations in the light chain, and separately analyze their simultaneous presence in all chains.
Start selecting flexible Antigen chains right now!
Monthly payment for selection of flexible chains Antibodies to Antigen 349 Euro, up to 20 options the work will take 3-4 weeks, over 50 variants the work will take 2-4 months.
