Abstract: A method for predicting drug-target binding using synthetically-augmented data involves generating a multitude of ghost ligands for a multitude of proteins in a protein structure database, generating a multitude of drug-target interaction (DTI) features for proteins and ligands in a DTI database, using the multitude of ghost ligands, generating a machine learning model using the multitude of DTI features, and predicting a likelihood of interaction for a combination of a query protein and a query ligand using the machine learning model.

Abstract: A method for predicting a property of a sample molecule involves, for each of a multitude of reference molecules, obtaining a multitude of fingerprints and at least one property, and obtaining the multitude of fingerprints of the sample molecule. The method further involves for each of the multitude of reference molecules, using each of the multitude of fingerprints, calculating distances to the sample molecule, and for each of the multitude of reference molecules, determining a relative predictive dominance, based on the distances to the sample molecule. The method also involves, for each of the multitude of reference molecules, determining a fitness value based on the relative predictive dominance, and predicting the at least one property of the sample molecule based on the at least one property of the multitude of reference molecules and the fitness values obtained for the reference molecules.

Abstract: The present invention provides, among other things, methods, compositions and systems for highly efficient, robust, multiplex analysis of biomolecules based on substrate-mediated compartmentalization in conjunction with controlled release of assay reagents for interference-free detection of biomolecules.

Abstract: A method for differential drug discovery involves obtaining a receptor panel. The receptor panel specifies a multitude of targets and a multitude of anti-targets. The method further involves obtaining a small molecule compound (SMC) seed model and derivatizing a first multitude of candidate SMCs from the SMC seed model. For each of the candidate SMCs in the first multitude of candidate SMCs, first desired interactions between the candidate SMC and each of the multitude of targets are simulated. Further, for each of the candidate SMCs in the first multitude of candidate SMCs, first undesired interactions between the candidate SMC and each of the multitude of anti-targets are simulated.

Abstract: The present invention provides, among other things, methods, compositions and systems for highly efficient, robust, multiplex analysis of biomolecules based on substrate-mediated compartmentalization in conjunction with controlled release of as-say reagents for interference-free detection of biomolecules.

Abstract: Disclosed herein are compositions and methods relevant to a novel Drug Metabolism Reserve Physiotype to determine the metabolic capacity of a human individual. The Drug Metabolism Reserve Physiotype allows the determination of the innate metabolic capacity of the patient relevant to antidepressant and stimulant treatment and can be predicted and diagnosed simply from a blood sample. In the disclosed method, an individual is genotyped for a plurality of polymorphisms in a gene encoding CYP2C9, a gene encoding CYP2C19 and a gene encoding CYP2D6, and the genotypes are used to produce four novel indices, which relate to the metabolic capacity of the human individual.

Abstract: Disclosed herein are compositions and methods relevant to a novel Drug Metabolism Reserve Physiotype to determine the metabolic capacity of a human individual. The Drug Metabolism Reserve Physiotype allows the determination of the innate metabolic capacity of the patient relevant to antidepressant and stimulant treatment and can be predicted and diagnosed simply from a blood sample. In the disclosed method, an individual is genotyped for a plurality of polymorphisms in a gene encoding CYP2C9, a gene encoding CYP2C19 and a gene encoding CYP2D6, and the genotypes are used to produce four novel indices, which relate to the metabolic capacity of the human individual.

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

Abstract: The present invention provides, among other things, methods and systems for characterizing multifunctional objects using a flow-through device, such as, a flow cytometer. In some embodiments, an inventive method according to the present invention includes one more steps of (a) interrogating a plurality of objects (e.g., particles), wherein each individual object (e.g., particle) comprises one or more interrogation regions detectable as a sequence of events; (b) recording multiple events, wherein each individual event corresponds to each individual interrogation region detectable above a pre-determined triggering threshold; (c) grouping the recorded multiple events, and (d) characterizing the plurality of objects based on the grouped events.

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

Abstract: In certain embodiments, the invention relates to systems, methods, and apparatus that allow a purchaser to customize a test kit based upon a literature search. A processor receives one or more search terms entered by a user and constructs a query comprising the one or more search terms. The processor obtains from one or more literature repositories a plurality of search results responsive to the query. The processor identifies one or more domain terms (relating to a scientific domain) within the plurality of search results. The processor prioritizes the one or more scientific domain terms based in part upon frequency of occurrence within the plurality of search results, and selects one or more order components relating to a tangible product, each order component relating to a respective scientific domain term of the one or more scientific domain terms. The order information is displayed to a user.

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

Abstract: A method may include accessing data regarding a number of events, where the events were detected by a particle detection apparatus, and identifying a number of groups in the events. Each of the groups includes two or more events, and each event includes one or more of a time stamp, a time duration, a fluorescence intensity, a scatter measurement, a radio frequency signal, a magnetic signal, a neutron scattering measurement, a light scattering measurement, an electron scattering measurement, an audio signal, an acoustic signal, a mechanical signal, an electrical resistance, a thermal property, and a width of fluorescence signal. The method may include identifying a subset of the groups as a number of objects detected by the particle detection apparatus, where each object is identified based at least in part upon one or more quantities, where each quantity is identified by or derived from the respective two or more events.

Abstract: The present invention provides, among other things, methods and systems for characterizing multifunctional objects using a flow-through device, such as, a flow cytometer. In some embodiments, an inventive method according to the present invention includes one more steps of (a) interrogating a plurality of objects (e.g., particles), wherein each individual object (e.g., particle) comprises one or more interrogation regions detectable as a sequence of events; (b) recording multiple events, wherein each individual event corresponds to each individual interrogation region detectable above a pre-determined triggering threshold; (c) grouping the recorded multiple events, and (d) characterizing the plurality of objects based on the grouped events.

Abstract: Disclosed herein are genetic markers related to the efficacy and/or safety of thiazolidinedione therapy identified by a physiogenomic methodology that correlates the genetic markers with a physiological response. The genetic markers described herein were not previously associated with the efficacy and/or safety of thiazolidinedione therapy. The markers related to safety are those associated with the important side effects of BMI increase and development of edema. In one embodiment, markers related to efficacy of thiazolidinedione therapy are associated with glycosylated hemoglobin. Method of assessing an individual for markers associated with the safety and/or efficacy of thiazolidinedione therapy are described.

Abstract: The invention is generally directed to a physiogenomic method for predicting diabetes and metabolic syndromes induced by psychotropic drugs. In one embodiment, the invention relates to the use of genetic variants of marker genes to predict the likelihood that an individual will experience undesirable metabolic side effects as a result of the use of a drug including, but not limited to, psychotropic drugs. The invention also relates to methods predicting the likelihood of diabetes and metabolic syndromes induced by the use of drugs with undesirable metabolic side effects.

Abstract: The present invention provides, among other things, methods and compositions for detecting and quantifying target nucleic acids via post-hybridization labeling.

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

Abstract: The invention is generally directed to a physiogenomic method for predicting diabetes and metabolic syndromes induced by psychotropic drugs. In one embodiment, the invention relates to the use of genetic variants of marker genes to predict the likelihood that an individual will experience undesirable metabolic side effects as a result of the use of a drug including, but not limited to, psychotropic drugs. The invention also relates to methods predicting the likelihood of diabetes and metabolic syndromes induced by the use of drugs with undesirable metabolic side effects.