Methods and compositions are disclosed for rapid functional analysis of gene variants based on analysis of protein-protein and protein-nucleic acid interactions.

Methods for producing high concentration protein formulations having high stability are provided. Assays for selecting proteins and formulation conditions that have high self-repulsive attributes are used as an early step in the manufacturing process. Specifically, a protein concentration-dependent self-interaction nanoparticle spectroscopy method is employed as a protein colloidal interaction assay.

The invention provides a novel integrated structure and system-based approach for drug target prediction that enables the large-scale discovery of new targets for existing drugs Novel computer-readable storage media and computer systems are also provided. Methods and systems of the invention use novel sequence order-independent structure alignment, hierarchical clustering, and probabilistic sequence similarity techniques to construct a probabilistic pocket ensemble (PPE) that captures even promiscuous structural features of different binding sites for a drug on known targets. The drug's PPE is combined with an approximation of the drug delivery profile to facilitate large-scale prediction of novel drug-protein interactions with several applications to biological research and drug development.

The invention provides methods and compositions useful for identifying polypeptides with desired characteristics in vitro.

The present invention is useful in screening for biomarkers associated with any other disease or condition. Such diseases and conditions range from the neurological diseases, autoimmune diseases and cancers identified above as well as any other disease or condition that has a biomarker such as an antibody or other characterizing protein or biomolecule associated with the disease or progression of the disease. The large ligand libraries of the invention can be used directly in biological fluid, under the appropriate experimental conditions and according to the processes recited herein, to screen for such markers and without the need to use fewer support members (e.g. about 100,000 or less) or without the need to transfer such peptoids or ligands to a microarray before screening the biological fluid. In addition, the ligand libraries may also be used to screen for cell based receptors that specifically relate to a particular cell surface marker.

Methods of identifying cancer/testes antigens (CTAs) useful as cancer treatment targets are disclosed and claimed herein. The methods include identifying human sperm proteins to which patients diagnosed with solid or hematological malignancies have established a humoral immune response.

The invention provides a BASEHIT screening method for identifying proteins that are involved in host-microbe interactions which may function as therapeutic targets.

A method of preventively treating a subject at the risk of developing infections of a respiratory virus is disclosed. The method includes a step of administering to the subject an effective amount of a peptide synthesized through a chemical route or by a genetic engineering process, characterized in that the peptide has a functional domain capable of binding to a surface glycoprotein of a respiratory virus and has an activity of inhibiting infection of the respiratory virus, wherein the peptide has 5 or more basic amino acids, among which 2 or more basic amino acids are in N-terminal region or C-terminal region of the peptide; and wherein the peptide consists of an amino acid sequence that is at least 90% identical to SEQ ID NO: 10. The invention also discloses the mechanism of the peptides in inhibition of said infections, which provides theory support for developing new prophylactic/therapeutic agents with broad-spectrum antiviral activities.

The present application relates, in some aspects, to the development of a plasmid that can be used to efficiently monitor the stabilities of thousands of proteins after specific perturbations. The plasmid allows for the co-expression of two reporter proteins, each of which is placed under the control of an IRES. Other aspects of the invention relate to a plasmid library, screening methods to identify proteins whose levels are modulated by a compound of interest, and methods for monitoring treatment of a subject with an IMiD compound.

The present disclosure relates to a system for monitoring post-translational modification of protein using a biosensor with a gap, which performs with high reliability a diagnosis of a disease associated with a target protein for which impedance is measured, by measuring an impedance of a sample introduced into a sensor and calculating a change rate of the measured impedance, and to a method of manufacturing the biosensor used for the system.