Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.

The present invention relates to a top-down symmetric deconstruction approach which provides a novel alternative means to successfully identify a useful polypeptide “building block” for subsequent “bottom-up” de novo design of target protein architecture. The present invention also pertains to a novel peptides isolated by top-down symmetric deconstruction which may be useful for design or directed evolution of novel proteins with novel functionalities.

The present application is directed to methods and systems for identifying small molecule compounds in mixtures using a library comprising calculated structures and corresponding calculated mass spectral fragmentation patterns of known and/or hypothetical small molecule compounds that may be in the mixture and screening of a mass spectrum of the mixture using the library to identify matching fragmentation patterns. If a mass spectral fragmentation pattern present in the mass spectrum of the mixture matches a calculated fragmentation pattern of one of the known or hypothetical compounds this confirms the identity of a compound in the mixture as the known or hypothetical compound. The method represents a platform method that can be used for a multitude of purposes related to the screening and identification of compounds in mixtures. Therefore the methods and systems of the present application represent an approach that is uniquely capable of navigating chemical space and providing a understanding of desired families and pharmacophores.

The present disclosure provides, among other things, novel cyclic-GMP-AMP (cGAMP) analogs, mimics, mimetics and variants, and compositions and kits thereof; methods of using the compounds as described herein for treating cancer, and immune disease, disorders, or conditions; methods of using the compounds as described herein for modulating cGAS and STING; and methods of designing or characterizing a cGAS modulator.

Systems and methods to provide augmented and virtual reality implementations of information sources useful as learning and discovery tools are disclosed. A computer implemented method and programming product which provides enhanced visualization of various information resources useful for at least teaching and learning, drug research and discovery, and precision and personalized medicine. A computer-implemented method and programming product for providing medication and/or appointment reminder, alerts, and education is also provided. These cross platform software applications use graphic processing unit (GPU) accelerated big data analysis algorithms, and innovative natural language processing (NLP) algorithms to improve user experiences and access to the information resources.

Systems and methods to provide augmented and virtual reality implementations of information sources useful as learning and discovery tools are disclosed. A computer implemented method and programming product which provides enhanced visualization of various information resources useful for at least teaching and learning, drug research and discovery, and precision and personalized medicine. A computer-implemented method and programming product for providing medication and/or appointment reminder, alerts, and education is also provided. These cross platform software applications use graphic processing unit (GPU) accelerated big data analysis algorithms, and innovative natural language processing (NLP) algorithms to improve user experiences and access to the information resources.

The invention relates to methods for modulating the immune function through targeting of CLIP molecules. The result is wide range of new therapeutic regimens for treating, inhibiting the development of, or otherwise dealing with, a multitude of illnesses and conditions, including autoimmune disease, cancer, Alzheimer's disease, allergic disease, transplant and cell graft rejection, HIV infection and other viral, bacterial, and parasitic infection, and AIDS. Methods are also provided for preparing a peptide having the property of being able to displace CLIP by feeding one or more peptide sequences into software that predicts MHC Class II binding regions in an antigen sequence and related products.

In some embodiments, the present invention provides method of identifying compounds that bind to phosphoinositol 4-phosphate adaptor protein-2 (FAPP2), including the steps of computationally identifying a compound that binds to FAPP2 using the atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2. Also provided are methods of designing, selecting and/or optimizing a compound that binds to FAPP2.

The present invention relates to the discovery of a method for identifying a treatment regimen for a patient diagnosed with cancer, predicting patient resistance to therapeutic agents and identifying new therapeutic agents, obtaining the specificity profile of a therapeutic agent, a method of designing a scaffold of a therapeutic agent directed against a drug-resistant target, drug scaffolds, and methods of uses thereof to identify drugs to treat diseases such as cancer. Specifically, the present invention relates to the use of an algorithm to identify a mutation in a kinase, determine if the mutation is an activation or resistance mutation and then to suggest an appropriate therapeutic regimen. The invention also relates to the use of a pattern matching algorithm and a crystal structure library to predict the functionality of a gene mutation, predict the specificity of small molecule kinase inhibitors and for the identification of new therapeutic agents.

The present invention relates to the discovery of a method for identifying a treatment regimen for a patient diagnosed with cancer, predicting patient resistance to therapeutic agents and identifying new therapeutic agents, obtaining the specificity profile of a therapeutic agent, a method of designing a scaffold of a therapeutic agent directed against a drug-resistant target, drug scaffolds, and methods of uses thereof to identify drugs to treat diseases such as cancer. Specifically, the present invention relates to the use of an algorithm to identify a mutation in a kinase, determine if the mutation is an activation or resistance mutation and then to suggest an appropriate therapeutic regimen. The invention also relates to the use of a pattern matching algorithm and a crystal structure library to predict the functionality of a gene mutation, predict the specificity of small molecule kinase inhibitors and for the identification of new therapeutic agents.