Methods and applications for relating the structure of a molecule in a library to its function are described. Embodiments described herein relate structure to function by considering the covalent structure of the molecule, the components of that structure that are common to many molecules in the library, and the properties of those components as they relate to the function in question. Applications include, for example, enhancement and amplification of the diagnostic and prognostic signals provided by peptide arrays for use in analyzing the profile of antibodies in the blood produced in response to a disease, condition or treatment.

The present disclosure relates to methods for screening for a modulator of a target protein. The present disclosure further relates to a systematic disease drug repositioning (SMART) method which integrates experimental and computational biology methods systematically with public transcriptomic profile data to enable fast-track identification and confirmation of novel drug candidates.

Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.

The invention generally relates to systems methods for screening a sample based on multiple reaction monitoring mass spectrometry. In certain embodiments, the invention provides methods for screening a sample that involve ionizing a sample. Mass spectrometry is then used in order to monitor specific transitions connecting one or more ion pairs within the sample in order to generate a multidimensional chemical profile of the sample. Then, the multidimensional chemical profile of the sample is compared to a database of reference multidimensional chemical profiles, thereby screening the sample. Each reference multidimensional chemical profile is produced from a training set of data.

A platform configured to predict type or family of an unknown drug candidate compound, the platform including: a living cell or a tissue; a detector that measures an indicator of a cellular response by the living cell or tissue upon exposure to the unknown drug candidate compound; a memory configured to store data related to the indicator of the cellular response detected by the detector from a library of drug types and/or families; and one or more processing unit(s) configured to: process the data related to the indicator of the cellular response of the living cell or tissue upon exposure to the unknown drug candidate compound, and compare cellular response data from the library of drug types and/or families, so that a drug type and/or a drug family and/or a mechanism of action of the unknown drug candidate compound can be predicted on the basis of a similarity between the detected cellular response data of the unknown drug candidate compound and the cellular response data of the library of drug types and/or families. Also disclosed are methods of screening an unknown drug, including: comparing the data measured from a test cell to corresponding cellular response data in a library of known drug types, and determining a relationship between the unknown drug and a known drug type or a known drug family to predict the type or family of the unknown drug.

The present disclosure relates to a method and apparatus for identification of similar species, and more particularly to method and apparatus for identification of similar species based on machine learning using negative markers. According to an aspect of the present disclosure, a method for identifying similar species may comprise: extracting first mass information for an input sample; classifying the input sample using a machine learning model based on at least a negative marker, based on the first mass information; and identifying a species for the input sample based on the classification result.

The invention provides compositions and methods for treating cardiac dysfunction, particularly cachexia-associated or RAGE-associated cardiac dysfunction, using an anti-RAGE agent. The invention also provides compositions and methods for identifying therapeutic agents useful for disrupting (slowing, reducing, reversing, or preventing). The methods comprise designing or identifying agents that bind to functional sites identified on the RAGE polypeptide, wherein binding of agents to the functional site(s) inhibit RAGE-mediated cachetogenic signaling.

A method of chemical process simulation includes providing a Sequential-Modular process simulator having a simulation algorithm. Responsive to receiving a process flowsheet creating a directed graph (DG) which represents a topology of the process flowsheet with components interconnected as nodes and process streams including recycle streams represented as cycles, with dependencies between process streams adding cycles. Partitioning the components into a first portion including strongly-connected component groups (SCCGs) along with individual components. An initial location is provided for each cycles for the SCCGs to generate a directed acyclic graph (DAG). An initial calculation order is determined for the flowsheet from the DAG, including an order for calculation within the SCCGs themselves. The SCCGs and components as nodes and process streams as edges with a graphical indication representing each cycle for the SCCGs along with the initial calculation order are graphically displayed, wherein the initial calculation order is user modifiable.

The method comprises performing the following steps by means of processing representative data of the flexible porous structure: a) generating a first function (F.sub.s) defining how the flexible porous structure changes shape when it is subjected to deformation; b) generating a second function (F.sub.p) defining how a covered surface of the flexible porous structure changes when it is subjected to changes in shape; c) obtaining, by means of said function (F.sub.s), reference porosity values of a reference region (CU-R) of the flexible porous structure in a reference configuration; and d) calculating the porosity of at least one deformed region (CU-D) of the flexible porous structure, from said reference porosity values and from said second function (F.sub.p).

The present application relates to a method for quantitative analysis of a polymer structure. Specifically, the method may be carried out through steps of measuring rheological properties and/or molecular weight distribution of the arbitrarily selected polymer, setting a random value for the selected polymer and then predicting the rheological property and/or the molecular weight distribution of the polymer from the random value, and comparing the measured value with the predicted value to determine the value of the structural parameter of the polymer.