Abstract: Multivalent D-peptidic compounds that specifically bind to a target protein are provided. The multivalent D-peptidic compounds can include two or more distinct variant D-peptidic domains connected via linking components. The D-peptidic compounds can include multiple distinct domains that specifically bind to different binding sites on a target protein to provide for high affinity binding to, and potent activity against, the target protein. D-peptidic variant GA and Z domain polypeptides are also provided, which polypeptides have specificity-determining motifs (SDM) for specific binding to a target protein, such as VEGF-A or PD-1. In some embodiments where the target protein is homodimeric (e.g., VEGF-A, PD-1), the D-peptidic compounds may be similarly dimeric, and include a dimer of multivalent (e.g., bivalent) D-peptidic compounds. Methods for using the compounds are provided, including methods for treating a disease or condition associated with a target protein in a subject.

Abstract: D-peptidic compounds that specifically bind to VEGF are provided. Also provided are multivalent D-peptidic compounds that include two or more of the domains connected via linking components. The multivalent (e.g., bivalent, trivalent, tetravalent, etc.) compounds can include multiple distinct domains that specifically bind to different binding sites on a target protein to provide for high affinity binding to, and potent activity against, the VEGF target protein. D-peptidic GA and Z domains that find use in the multivalent compounds are also provided, which polypeptides have specificity-determining motifs (SDM) for specific binding to VEGF (e.g., VEGF-A). Since the target protein is homodimeric (e.g., VEGF-A), the D-peptidic compounds may be similarly dimeric, and include a dimer of multivalent (e.g., bivalent) D-peptidic compounds. Also provided are methods for treating a disease or condition associated with VEGF or angiogenesis in a subject such as age-related macular degeneration (AMD) or cancer.

Abstract: GB1 peptidic compounds that specifically bind to a hemagglutinin target protein, and libraries that include the same, as well as methods of making and using the same, are provided. Also provided are methods and compositions for making and using the compounds. Also provided are hemagglutinin mimics and fragments and methods of using the same, including methods of screening for GB1 peptidic compounds and methods of using conjugates the mimics as influenza A vaccines. Aspects of the invention include methods of screening libraries of L-peptidic compounds for specific binding to a D-peptidic hemagglutinin target protein. Once a L-peptidic compound has been identified that specifically binds to the D-peptidic hemagglutinin target protein, the D-enantiomer of the selected L-peptidic compound may be produced. In some embodiments, the D-enantiomer of the selected L-peptidic compound binds to, and in some instances, neutralizes influenza virus particles.

Abstract: Methods and compositions for identifying D-peptidic compounds that specifically bind target proteins are provided. Aspects of the methods include screening libraries of 20 residue or more L-peptidic compounds for specific binding to 40 residue or more D-target proteins. Once a L-peptidic compound has been identified that specifically binds to the D-target protein, the D-enantiomer of that compound may be produced.

Abstract: GB1 peptidic compounds that specifically bind to a hemagglutinin target protein, and libraries that include the same, as well as methods of making and using the same, are provided. Also provided are methods and compositions for making and using the compounds. Also provided are hemagglutinin mimics and fragments and methods of using the same, including methods of screening for GB1 peptidic compounds and methods of using conjugates the mimics as influenza A vaccines. Aspects of the invention include methods of screening libraries of L-peptidic compounds for specific binding to a D-peptidic hemagglutinin target protein. Once a L-peptidic compound has been identified that specifically binds to the D-peptidic hemagglutinin target protein, the D-enantiomer of the selected L-peptidic compound may be produced. In some embodiments, the D-enantiomer of the selected L-peptidic compound binds to, and in some instances, neutralizes influenza virus particles.

Abstract: GB1 peptidic compounds that specifically bind to a hemagglutinin target protein, and libraries that include the same, as well as methods of making and using the same, are provided. Also provided are methods and compositions for making and using the compounds. Also provided are hemagglutinin mimics and fragments and methods of using the same, including methods of screening for GB1 peptidic compounds and methods of using conjugates the mimics as influenza A vaccines. Aspects of the invention include methods of screening libraries of L-peptidic compounds for specific binding to a D-peptidic hemagglutinin target protein. Once a L-peptidic compound has been identified that specifically binds to the D-peptidic hemagglutinin target protein, the D-enantiomer of the selected L-peptidic compound may be produced. In some embodiments, the D-enantiomer of the selected L-peptidic compound binds to, and in some instances, neutralizes influenza virus particles.

Abstract: Methods and compositions for identifying D-peptidic compounds that specifically bind target proteins are provided. Aspects of the methods include screening libraries of 20 residue or more L-peptidic compounds for specific binding to 40 residue or more D-target proteins. Once a L-peptidic compound has been identified that specifically binds to the D-target protein, the D-enantiomer of that compound may be produced.

Abstract: Methods and compositions for identifying D-peptidic compounds that specifically bind target proteins are provided. Aspects of the methods include screening libraries of 20 residue or more L-peptidic compounds for specific binding to 40 residue or more D-target proteins. Once a L-peptidic compound has been identified that specifically binds to the D-target protein, the D-enantiomer of that compound may be produced.

Abstract: Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

Abstract: Methods and devices for the parallel, in vitro screening of biomolecular activity using miniaturized microfabricated devices are provided. The biomolecules that can be immobilized on the surface of the devices of the present invention include proteins, polypeptides, nucleic acids, polysaccharides, phospholipids, and related unnatural polymers of biological relevance. These devices are useful in high-throughput drug screening and clinical diagnostics and are preferably used for the parallel screening of families of related proteins.

Abstract: Methods and devices for the parallel, in vitro screening of biomolecular activity using miniaturized microfabricated devices are provided. The biomolecules immobilized on the surface of the devices of the present invention include proteins, polypeptides, polynucleotides, polysaccharides, phospholipids, and related unnatural polymers of biological relevance. These devices are useful drug development, functional proteomics and clinical diagnostics and are preferably used for the parallel screening of families of related proteins.

Abstract: Methods for evenly distributing tags on collections of molecules are provided. Also provided are assay methods that employ the tagged collections.

Abstract: Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

Abstract: Therapeutic complexes and components of therapeutic complexes are provided herein. Also provided are methods of preparing therapeutic complexes and methods of administering therapeutic complexes.

Abstract: Collections of highly antigenic highly specific polypeptides are provided herein. Also provided are methods of generating collections of highly antigenic highly specific polypeptides and methods of synthesizing such collections.

Abstract: Cell based methods designed to assess intracellular and extracellular activities and interactions and to identify compounds and conditions that modulate such activities and interactions are provided. The cell based methods employ capture systems that display collections of tagged molecules specifically linked to capture agents.

Abstract: Protein arrays and protein-coated substrates for the parallel, in vitro screening of biomolecular activity are provided. Methods of using the protein-coated substrates and protein arrays are also disclosed. A plurality of different members of a single protein family may be immobilized on the protein-coated substrate or array. The protein-coated substrates and protein arrays are particularly useful in high-throughput drug screening and clinical diagnostics.

Abstract: Protein arrays and protein-coated substrates for the parallel, in vitro screening of biomolecular activity are provided. Methods of using the protein-coated substrates and protein arrays are also disclosed. A plurality of different members of a single protein family may be immobilized on the protein-coated substrate or array. The protein-coated substrates and protein arrays are particularly useful in high-throughput drug screening and clinical diagnostics.

Abstract: Provided herein are methods, combinations, kits and systems for self-assembly of a self-assembling array to produce self-assembled arrays. The self-assembling arrays contain addressed collections of capture agents and are used with binding partners and reagents for conjugation of binding partners to molecules and/or biological particles for display in self-assembled arrays. The capture agents at each locus in a self-assembling array are specific to one of a set of binding partner molecules. The binding partners are conjugated to molecules and/or biological particles for display. Following conjugation, the resulting conjugates are sorted on the array based on the specific interaction of the binding partner and the capture agent to produce a self-assembled array.

Abstract: Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.