Abstract: A proteome analysis method includes using a tandem type mass spectrometer to calculate bond dissociation energy by using molecular simulation, using the bond dissociation energy to obtain prediction information including a cleavage pattern of a peptide and/or peak positions in a mass spectrum and/or the intensity ratio of the mass spectrum, and identifying a protein by using the prediction information and experiment information.

Abstract: Disclosed is a method for predicting the biological activity of a compound by the similarity of its drug signature score to the scores of a plurality of known drug signatures.

Abstract: The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

Abstract: The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known cardiotoxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

Abstract: The present invention is in the field of bioinformatics, particularly as it pertains to gene prediction. More specifically, the invention relates to the probabilistic analysis of nucleic acid sequences for the determination of coding features, including determination of state probabilities for each nucleotide in a nucleic acid sequence, determination of coding strand, determination of open reading frame extent, determination of insertion and deletion location, determination of exon location, and determination of protein sequence.

Abstract: The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known renal toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

Abstract: The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known renal toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

Abstract: A method and device are described for analyzing a sample for the presence of a nucleic acid wherein the sample is amplified, illustratively using PCR, in the presence of a fluorescent probe capable of providing a signal related to the quantity of nucleic acid present. A nucleic acid sample is amplified in the presence of the fluorescent entity, and the fluorescence intensity is measured at each of a plurality of amplification cycles. Scores are obtained from various tests performed on the fluorescence data, and the scores are used to determine whether the nucleic acid is present in the sample.

Abstract: The present invention relates to polypeptides which comprise the ligand binding domain of Tie-2, crystalline forms of these polypeptides and the use of these crystalline forms to determine the three dimensional structure of the catalytic domain of Tie-2. The invention also relates to the use of the three dimensional structure of the Tie-2 catalytic domain both alone, or in complex with inhibitors, in methods of designing and/or identifying potential inhibitors of Tie-2 activity, for example, compounds which inhibit the binding of a native substrate to the Tie-2 catalytic domain.

Abstract: A method for determining the masses of ions of a sample that contains a known class of biopolymers and is measured with a mass spectrometer having a statistical or pseudo-statistical error distribution includes acquiring a mass spectrum of ions of biopolymers of the known class in the sample in which mass spectrum the mass values of ions of biopolymers from the known class are concentrated in known distributions around a set of most probable mass values. At least one measured mass value of the mass spectrum is replaced by that one of a set of most probable mass values that is nearest to the measured mass value, or by a weighted average of the measured mass value averaged with that one of the set of most probable mass values that is nearest to the measured mass value.

Abstract: The present invention relates to a novel method for the identification of candidate proteins in pathogens useful as anti-infectives and more particularly, the present invention describes a novel computational method involving calculation of several sequence attributes and their subsequent analysis lead to the identification of some outlier proteins in different pathogens which are either vaccine candidates, diagnostics or drug targets and also are provided the genes encoding the candidate proteins.

Abstract: A molecular motor in which multiple concentric cylinders (or nested cones) rotate around a common longitudinal axis. Opposing complementary surfaces of the cylinders or cones are coated with complementary motor protein pairs (such as actin and myosin). The actin and myosin interact with one another in the presence of ATP to rotate the cylinders or cones relative to one another, and this rotational energy is harnessed to produce work. The concentration of ATP and the number of nested cylinders or cones can be used to control the rotational speed of the motor. The length of the cylinders can also be used to control the power generated by the motor. In another embodiment, the molecular motor includes at least two annular substrates wherein one annular substrate is coated with a first motor protein and the other annular substrate is coated with a second motor protein. The first and second motor proteins interact with each other to move the second annular relative to the first annular substrate.

Abstract: A method for non-targeted complex sample analysis which involves the following steps. A first step involves providing a data base containing identifying data of known molecules. A second step involves introducing a complex sample containing multiple unidentified molecules into a Fourier Transform Ion Cyclotron Mass Spectrometer to obtain data regarding the molecules in the complex sample. A third step involves comparing the collected data regarding the molecules in the complex sample with the identifying data of known molecules in order to arrive at an identification through comparison of molecules in the sample.

Abstract: A robust genotyping method using a DNA chip is provided. In the DNA chip used in the genotyping method, optimal probe pairs of a wild-perfect match probe and a mutant-perfect match probe are immobilized for each mutation site on a substrate. The method includes setting up a genotyping algorithm using data obtained from hybridization of an identified standard nucleic acid to the DNA chip, and genotyping an unknown target nucleic acid by substituting input vectors that are calculated from hybridization of the target nucleic acid to the DNA chip into the genotyping algorithm. The results of genotyping the target nucleic acid using the optimal probe pairs for each mutation site are statistically robust to errors.

Abstract: A method and system of comparing a query and a subject database using a distributed computing platform is disclosed. The databases are divided into data elements having a size within a specified range. All data elements and task definitions are sent to a master CPU of a master-slave distributed computing platform, wherein task definitions comprise at least one comparison parameter, at least one executable comparison element, and a query and a subject data element ID/descriptor. Data elements are sent alternately from query and subject data elements. A task definition is sent for each task from the master CPU to one of a plurality of slave CPUs when all parts of a task definition and data elements referenced by the task definition are available at the master CPU. Data elements are then sent to the slave CPUs for performance of the tasks. Task results for each task are returned to a CPU.

Abstract: A method predicts at least one property of a candidate molecule. A set of reference molecules is classified as either possessing or not possessing at least one property. A subset of the molecules is selected from which a plurality of marker molecules is chosen. The marker molecules are used to predict whether the candidate molecule possesses at least one property.

Abstract: A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.

Abstract: The present invention provides systems, methods, and screens for an optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a high magnification fluorescence optical system, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations.

Abstract: New cytokine polypeptides, and nucleic acids encoding them, are provided. Compositions including these polypeptides and nucleic acids, recombinant cells comprising said polypeptides and nucleic acids, methods of making the polypeptides and nucleic acid, antibodies to the polypeptides, and methods of using the polypeptides and nucleic acids are provided. Integrated systems comprising the sequences of the nucleic acids or polypeptides are also provided.

Abstract: The instant invention involves the use of a combination of preparatory steps in conjunction with mass spectroscopy and time-of-flight detection procedures to maximize the diversity of biopolymers which are verifiable within a particular sample. The cohort of biopolymers verified within such a sample is then viewed with reference to their ability to evidence at least one particular disease state; thereby enabling a diagnostician to gain the ability to characterize either the presence or absence of said at least one disease state relative to recognition of the presence and/or the absence of said biopolymer.