A method for T-cell epitope prediction where quantitative scores of stability in the binding between peptides and MHC molecules are integrated into the derivation of the likelihood that a peptide of defined amino acid sequence constitutes a T-cell epitope. Preferably, stability data are obtained an MS-based method for identification of MHC binding peptides, where the binding capability is quantitatively assessed to allow distinction between stably binding peptides and peptides that are unlikely to be presented to T-cells. The method includes a step of time-course or thermostability testing of naturally processed peptides bound to MHC. Also disclosed are methods for preparation of personalized immunogenic compositions, methods of therapeutic treatment of malignancies, and a computer system that implements the T-cell epitope prediction method.

Herein is reported a method for determining the epitope of an antibody specifically binding to a therapeutic antibody comprising the steps of a) incubating a sample, which comprises serum and the antibody specifically binding to a therapeutic antibody, separately with i) at least a Fab fragment of the therapeutic antibody, and ii) at least a Fab fragments of the therapeutic antibody in which the HVRs forming a paratope have been replaced with germline sequences, and detecting the binding or non-binding of the antibody specifically binding to a therapeutic antibody to the at least a Fab fragment in any of i) to ii), and b) determining the epitope of the antibody specifically binding to a therapeutic antibody to be in the at least one HVR that has been replaced in ii) if binding is detected in i) and non-binding is detected in ii).

The present invention is directed to a method for generating a library of antigen binding molecules for screening for binding to an epitope of interest, said method comprising: a. selecting a template antigen-binding molecule from a set of possible template antigen binding molecules wherein said selected template does not specifically bind the epitope of interest but is known to specifically bind another epitope; b. selecting at least one residue position in said template antigen-binding molecule for mutation; and c. selecting at least one variant residue to substitute at the at least one residue position selected in b; such that a library containing a plurality of variants of said template is generated.

Systems and methods are presented that allow for predicting treatment response of a tumor to a checkpoint inhibitor. In one exemplary aspect, the treatment response is directly associated with a relatively high number of patient- and tumor-specific immunologically visible neoepitopes. Specific mutational patterns in the nucleic acid encoding the neoepitope may be further indicative of treatment response.

The invention provides methods and compositions for identifying binding polypeptides (e.g., antibodies or antigen binding fragments thereof) that specifically binds to a cell-surface antigen. The methods of the invention generally comprise contacting a variegated nucleic acid-display library of binding polypeptides with a cell-surface antigen displayed on the exterior surface of a cell; and isolating from the library at least one library member that specifically binds to the cell-surface antigen on the exterior surface of the cell.

A method of broadening epitopic coverage of an antigen of interest, wherein a first sample of the antigen of interest is contacted with a first plurality of host cells collectively expressing a first library of antibodies. Host cells expressing antibodies that bind to the antigen are then collected from among the first plurality of host cells, and a composition is prepared comprising a polyclonal mixture of antibodies expressed by these host cells. A second sample of the antigen of interest is then contacted with an aliquot of the prepared composition and a second plurality of host cells collectively expressing a second library of antibodies. Host cells expressing antibodies that bind to the second sample of the antigen are then collected from among the second plurality of host cells.

Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.

Compositions and methods for isolating HLA-peptides from cells. A universal platform and methods for profiling the HLA-peptidome, enabling identification of endogenously presented HLA-peptides from cell lines expressing any possible class I or II construct.

Provided is a method and a device for screening an antigen epitope polypeptide. The screening method includes: predicting one or more antigen epitopes with all proteome sequences of a target coronavirus to obtain a predicted epitope region; screening a polypeptide with a differential response to a positive serum sample infected by the target coronavirus and a control serum sample with a polypeptide chip technology, and recording the polypeptide as a differential peptide fragment; comparing the differential peptide fragment with all proteome sequences of the target coronavirus to obtain a first conserved motif region; screening regions meeting epitope screening conditions from the predicted epitope region and the first conserved motif region to obtain the antigen epitope, wherein the epitope screening conditions comprise a non-phosphorylation region and/or an extracellular region of the target coronavirus.

The present disclosure relates to a method for determining the potency of an antigen sample such as a vaccine antigen sample. The present disclosure is also related to a method for monitoring the potency of a vaccine antigen during the production process including purifying, inactivating and formulating the vaccine antigen and to a method for producing a virus vaccine. Further, the present disclosure relates to vaccines obtainable by the methods disclosed. In certain embodiments of the present invention the antigen sample is a zika virus antigen sample.