Provided herein are methods, chemical library and simulation system for performing in situ patterned chemistry. Methods, systems and assays comprising the use of the synthesized chemical libraries, which increase explored protein space in a knowledge-based manner, are also provided for characterizing antibody-target interactions including: identifying target proteins of antibodies, characterizing antibody-binding regions in target proteins, identifying linear and structural epitopes in target proteins, and determining the propensity of antibody binding to target proteins.

Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

Methods for in situ detecting proximity of two targets of interest featuring an antibody conjugated with a cleavable bridge component having a detectable moiety and an antibody conjugated with a non-cleavable bridge component. The bridge components each have a chemical ligation group adapted to form a covalent bond under particular conditions and when the targets are in close proximity. Following covalent bond formation, the cleavable bridge component can be cleaved from the antibody, effectively transferring the detectable moiety to the non-cleavable bridge component. Detection of the detectable moiety is indicative of the targets being in close proximity. The methods are compatible with both chromogenic and fluorogenic detection systems. The methods may be used to perform assays wherein one or more than one proximity event is detected on the same slide.

A method for screening for a molecule capable of forming a complex with a plurality of target molecules has been found by applying an affinity-based method for recovering a candidate molecule to techniques represented by Split GFP techniques. The method includes allowing a first target molecule linked to a first moiety of a protein, a second target molecule linked to a second moiety of the protein, and a library containing a plurality of test molecules to coexist, and recovering a test molecule capable of forming a complex with the first target molecule linked to the first moiety and the second target molecule linked to the second moiety by an affinity technique.

A method for high-throughput screening of a chimeric antigen receptor (CAR) cell library is provided comprising the steps of (a) providing a recognition sequence library, a hinge region sequence library, a transmembrane sequence library and an intracellular domain sequence library; (b) preparing a CAR library; (c) preparing a CAR-cell library by introduction to, and expression of, the plurality of CAR sequences of the CAR library in one or more cells or a cell line; (d) screening the CAR-cell library in an assay; (e) evaluating the at least one function of each member of the CAR-cell library; (f) obtaining one or more sequences of one or more CARs expressed in the CAR-cell library and linking the obtained sequence(s) to the at least one function of the members of the CAR-cell library; g) identifying and selecting the or each sequence based on function. Methods of preparing the CAR library and a CAR-cell library and uses thereof are also provided.

This application provides an improved screening method for the selection of target-binding proteins having desirable biophysical properties. The method combines mRNA display and yeast surface display in a way that takes advantage of the desirable attributes of both processes.

Methods and systems for performing assays in compartmentalized nano-volumes to screen for functional bispecific or multispecific biologics, including: providing a plurality of at least two distinct types of cells, wherein two or more first-type cells are engineered to express substantially a single genetic-variant per cell for a bispecific or multispecific biologic in a secreted form, wherein two or more second-type cells are selected or engineered to produce a positive reporter molecule signal that is triggered by a functional variant of the said biologic expressed by a first-type cell; providing a plurality of compartmentalized nano-volumes, wherein two or more nano-volumes are each provided with substantially one first-type cell, and one or more second-type cell(s); incubating the said nano-volumes over a period of time to allow the expression and secretion of the said biologics inside the said nano-volumes; collecting data representing the positive reporter molecule signal triggered by secreted biologics inside the said nano-volumes, and recovering cells from the nano-volumes with the positive reporter molecule signal and extracting the genetic information representing respective functional variants of the biologics.

Provided herein are methods, systems, kits, and compositions useful for determining small molecule-protein interactions and protein-protein interactions. The photo-click tags provided herein can be conjugated to a small molecule or amino acid analog to provide compounds that can be integrated into a protein through photo-conjugation, allowing for identification of a small molecule-protein interaction or protein-protein interaction to elucidate the small molecules mechanism of action or the protein targeted by the small molecule. In some embodiments, the photo-click tags comprise a photo-conjugation moiety and a click chemistry handle, allowing for the attachment of various functional groups (e.g., affinity tags) to the small molecule or amino acid analog.

The present disclosure provides methods for measuring activity of cellular retinaldehyde-binding protein (CRALBP) or potency of a composition comprising an AAV vector comprising a CRALBP coding sequence for expressing a CRALBP protein. Also provided are kits for use in measuring activity of CRALBP.

A Method for selecting peptide inhibitors based on protein cytotoxicity by inserting a cytotoxic target protein and a library of peptide variants in a host cell, expressing the cytotoxic protein and peptide variants in the host cell, and identifying the peptide variants that block the cytotoxic target protein. The cytotoxic target protein is formed by synthesizing a cytotoxic protein gene and cloning the cytotoxic protein gene with an expression vector in a host cell. The library of peptide variants is formed by synthesizing a peptide library or building a peptide library using degenerate oligos and by cloning the peptide library with an expression vector in the host cell. Peptide variants are identified by identifying growing clones through growth on solid media or in a liquid culture. Both cyclic and linear peptides are produced. Intracellular biasing libraries of peptide variants produce inhibitor peptides with lower toxicity and higher stability compared to current methods.