Abstract: The present invention provides a single domain antibody (sdAb) scaffold comprising one or more than one non-canonical disulfide bond in the framework region (FR). The one or more than one non-canonical disulfide bond may be formed between cysteines introduced by mutations in FR2 and FR3. In the case where the sdAb scaffold is a VH, the Cys may be introduced at any one of positions (47-49) and any one of positions (67-71), based on Kabat numbering; in one example, the Cys may be introduced at positions (49) and (69), based on Kabat numbering. In the case where the sdAb scaffold is a VL, the Cys residues may be introduced at any one of positions 46-49 and any one of positions (62-66), based on Kabat numbering; in one example, the Cys residues may be introduced at positions (48 and 64), based on Kabat numbering.

Abstract: The present invention relates to a system and method for controlling peptide display valency on virus-like particles (VLPs), especially including MS2 VLPs. In this method, large amounts of wild-type and low quantities of single-chain dimer coat proteins may be produced from a single RNA. Valency is controlled in immunogen (vaccine) production by providing a system that allows the production of large amounts of wild-type and low quantities of single-chain dimer coating proteins from a single RNA, allowing facile adjustment of display valency levels on VLPs, especially MS2 VLPS over a wide range, from few than one—on average—to as many as ninety per particle. This facilitates the production of immunogens and vaccines, including VLPs exhibiting low valency.

Abstract: The present invention provides, in part, an antibody display system that simultaneously uses a secretion and a display mode. A bait complexed with a monovalent antibody fragment can be expressed on the surface of the host cell wherein the fragment may be assayed for antigen binding while full antibody is simultaneously secreted from the host cell. Methods of using the system for identifying antibodies that bind specifically to an antigen of interest are also provided. Polypeptides, polynucleotides and host cells useful for making the antibody display system are also provided along with methods of use thereof.

Abstract: The present invention provides a method for inducing a cancer specific immune response against MUC1 using an immunogenic glycopeptide. Other aspects of the invention are a pharmaceutical composition comprising the immunogenic glycopeptide and a cancer vaccine comprising the immunogenic glycopeptide. Another aspect is an antibody generated using the immunogenic glycopeptide and the use of said antibody in therapy and diagnosis.

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity.

Abstract: 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.

Abstract: A new biomarker, a peptide having sequence SSKITHRIHWESASLLR*, wherein the side chain of the C-terminal arginine denoted with the asterisk is lacking the NH2- C?NH moiety normally present in the side chain. Usefulness of the biomarker in the diagnosis of neurological and/or neuropsychiatric disorders (in particular autism) is disclosed, as well as are methods for determining the concentration of the new biomarker and antibodies directed to the new biomarker. Treatment of autism, comprising administering a complement factor I inhibitor to the subject.

Abstract: In a scanning system for the detection and discrimination of a plurality of targets in each of a plurality of samples, one or more multiband fluorescence detection channels each of which contains a single multiband emission filter and a single detector replaces multiple detection components in scanning heads of the prior art. In certain embodiments, a single multi-emitter light source is used as well, to illuminate each sample with excitation light at a variety of distinct wavelengths in succession.

Abstract: The invention provides single-chain Alphabody library comprising at least 100 different-sequence single-chain Alphabody polypeptides, wherein said Alphabody polypeptides differ from each other in at least one of a defined set of 5 to 20 variegated amino acid residue positions, and wherein at least 70% but not all of said variegated amino acid residue positions are located either in the loop, helix surface or linker region of the Alphabody. The invention further provides methods for use of the Alphabody libraries and Alphabodies obtainable by the methods of the invention.

Abstract: Disclosed are nucleic acid libraries for identifying a signal peptide that facilitates production of disulfide-stabilized single chain antibody, and for facilitating production of a disulfide-stabilized single chain antibody. Also disclosed are host cell libraries and phage libraries including the nucleic acid libraries. Further disclosed are methods for identifying a signal peptide that facilitates production of disulfide-stabilized single chain antibody, and methods for producing a disulfide-stabilized single chain antibody and non-fusion form thereof.

Abstract: The present invention relates to a method for preparing a target-specific non-antibody protein, and more particularly, to a method for preparing a target-specific non-antibody protein comprising the steps of: selecting non-antibody proteins having a structural complementarity with the target site of a target protein in a non-antibody protein library; calculating a binding energy of the selected non-antibody protein and the target protein; selecting a non-antibody protein having a favorable binding energy among the selected non-antibody proteins; selecting amino acid residues having a high binding energy among the interfacial amino acid residues of the selected non-antibody protein and the target protein; and substituting the selected amino acid residues with the amino acid residues having a low binding energy.

Abstract: A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 102, 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012 or more different sequences for a receptor of interest. Immunological receptors of interest include immunoglobulins, T cell antigen receptors, and major histocompatibility receptors. The specific composition of immunological receptor sequence variations in the sample can be recorded and output. The composition is useful for predictive, diagnostic and therapeutic methods relating to the immune capabilities and history of an individual. Such predictions and diagnoses are used to guide clinical decisions.

Abstract: The invention provides a method of producing a protein multimer-nucleic acid complex comprising a protein multimer and any one target component of the protein multimer. A nucleic acid encoding the target component is subjected to in vitro translation to provide a translation product containing a target component-nucleic acid complex of the target component and the nucleic acid encoding the target component. A nucleic acid encoding a non-target component constituting the protein multimer together with the target component is translated into the non-target component by adding the nucleic acid encoding the non-target component to the previously provided translation product to provide the non-target component. The non-target component then is associated with the target component contained in the target component-nucleic acid complex to form a protein multimer, thus affording the protein multimer-nucleic acid complex of the protein multimer and the nucleic acid encoding the target component.

Abstract: Disclosed are methods for identifying high affinity adaptor molecules that bind to both a circulating antibody and a target molecule and redirect the specificity of the circulating antibody to the target molecule. Exemplary high affinity adaptor molecules are also provided.

Abstract: The present invention provides antibody-based arrays for detecting the activation state and/or total amount of a plurality of signal transduction molecules in rare circulating cells and methods of use thereof for facilitating cancer prognosis and diagnosis and the design of personalized, targeted therapies.

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: A proteinaceous particle, for example a bacteriophage, ribosome or cell, displaying on its surface a T-cell receptor (TCR). The displayed TCR is preferably a heterodimer having a non-native disulfide bond between constant domain residues. Such display particles may be used for the creation of diverse TCR libraries for the identification of high affinity TCRs. Several high affinities are disclosed.

Abstract: The disclosure describes methods of identifying a variant of a reference antibody with reduced immunogenicity as compared to the reference antibody. The disclosure further describes variants of a reference anti-TNF-? antibody having reduced immunogenicity as compared to the reference anti-TNF-? reference antibody.

Abstract: Methods and systems for evaluating and predicting the reactivity of natural and engineered monooxygenase enzymes are provided. Methods are provided for acquiring a functional profile (fingerprint) of monooxygenases that encode information regarding the active site configuration of such monooxygenases. Methods are also provided for carrying out analysis of a monooxygenase fingerprint, to formulate predictions regarding the reactivity properties (e.g., substrate reactivity, chemo-, regio, and stereoselectivity properties) of the fingerprinted monooxygenases.

Abstract: The present invention relates generally to novel applications in combating infectious disease, cancer, allergy and autoimmune diseases. In one aspect, the invention relates to identifying one or more protein binding moieties of interest. In another aspect, the present invention relates to identifying one or more candidate vaccines.