High-throughput methods for screening large populations of variant proteins are provided. The methods utilize large-scale arrays of microcapillaries, where each microcapillary comprises a solution containing a variant protein, an immobilized target molecule, and a reporter element. Immobilized target molecules may include any molecule of interest, including proteins, nucleic acids, carbohydrates, and other biomolecules. The association of a variant protein with a molecular target is assessed by measuring a signal from the reporter element. The contents of microcapillaries identified in the assays as containing variant proteins of interest can be isolated, and cells expressing the variant proteins of interest can be characterized. Also provided are systems for performing the disclosed screening methods.

Bead arrays suitable for analysis by mass spectrometry are disclosed. In an embodiment, a bead array includes multiple reactive sites, each of the reactive sites being capable of binding multiple distinct target analytes.

Disclosed herein is a method of designing small peptides for interacting with, binding to, or modulating the activity of, known protein or peptides. Further disclosed herein are methods for selecting sequences likely to have high binding activity against known protein sequences as well as peptides derived from the disclosed methods.

Provided are methods of detecting and quantitatively measuring protein-protein interactions between proteins present on the surface of different cells using a sensitive antibody-based assay. Antibodies specific for each target protein are either directly labeled, or are detected by labeled secondary antibodies. The antibodies are labeled with detectable tags that are releasable when the target proteins are within proximity to each other. Also provided are methods for facilitating diagnosis, prognosis, and treatment of cancer using this assay to detect protein-protein interactions between target proteins of interest. Methods of screening test agents that impact the protein-protein interaction are also provided.

Embodiments of a method are disclosed for using molecular arrays (peptide arrays) to define networks of functionally linked molecules. This is accomplished via competition experiments in which molecules from the array are added to solution, specifically inhibiting the function (e.g. binding of an antibody) of the similar molecule in the array as well as any other molecules in the array that would have the same function. These networks of functionally linked molecules are very useful in both understanding the chemical nature of the function and in improving the statistical robustness of functional detection on the array, e.g. defining a robust immunosignature in an immunosignature application.

The present invention provides novel fluorescent dyes and kits containing the same, which are useful for labeling a wide variety of biomolecules, cells and microorganisms. The present invention also provides various methods of using the fluorescent dyes for research and development, forensic identification, environmental studies, diagnosis, prognosis and/or treatment of disease conditions.

The present invention provides an immunoassay leading to the rapid and simultaneous detection of antibodies to a wide range of infectious pathogens in biological fluids of infected patients. This immunoassay involves the covalent and oriented coupling of fusion proteins comprising an AGT enzyme and a viral antigen on an identifiable solid support (e.g. fluorescent microspheres). The thus obtained antigen-coupled microspheres show enhanced capture of specific antibodies as compared to antigen-coupled microspheres produced by standard amine coupling procedures.

The present invention relates to a reliable, robust and sensitive platform aimed to analyze the massive kinetic profile of new molecules against its main target and also against other potential targets. Thus, the present invention relates to a method for calculating the kinetic profile of a compound of interest against a target protein or polyprotein wherein it is not needed to predetermine the K.sub.i value of the compound of interest against the target protein or polyprotein before starting the assay. The present invention also discloses the use of said method in a high-throughput system for developing a Binding Kinetic Profiling assay of multiple compounds of interest against a unique target, or a

Kinetic Selectivity Profiling assay of one selected compound against multiple target proteins or polyproteins to therefore establish multiple clinical profiles of potential drugs.

An object of the present invention is to provide a method for identifying a physiologically active protein translated from an ORF other than mORF present on mRNA.

The object can be solved by a method for identifying a physiologically active protein, wherein an ORF which encodes a protein having a physiological activity, other than a main open reading frame (ORF) is identified in eukaryotic mRNA, comprising the steps of: (1) introducing an expression vector incorporating a candidate ORF to cells, and culturing the introduced cells, (2) detecting a protein bound to a candidate protein by immunoprecipitating the candidate protein translated from the candidate ORF, from the cultured cells, (3) determining a candidate protein in which another protein bound to the candidate protein is detected as a physiologically active protein.

The invention relates to methods for conducting solid-phase binding assays. One example is an assay method having improved analyte specificity where specificity is limited by the presence of non-specific binding interactions.