Abstract: A method of easily and speedily determining what structural change is experienced by a target protein upon contact and binding of any arbitrary compound to the target protein; a method of selecting and screening a compound for use in the method; and a computer program for carrying out these methods. In one embodiment, a Saupe order matrix element of domain is obtained from atomic coordinates of domain and an axial-direction variation of NMR signal dependent upon the orientation angle of molecule in magnetic field, and the matrix is diagonalized to thereby obtain the orientation information on the domain. Using of any change of the orientation information as an indicator for structural change enables realization of the intended easy and speedy measurement of structural change of the target protein.

Abstract: The invention provides methods and systems of determining biopolymer profiles and correlations between structural units (residues) of a biopolymer based on sampling of the conformational space available to the molecule. The correlations between these structural units can further be used to find networks within a biopolymer such as the coupled residue networks in a protein. The invention also provides for designing and engineering biopolymers including polypeptides, nucleic acids and carbohydrates using the information derived from the conformation clustering and subsequent methods described herein.

Abstract: The relationship between an amino acid sequence of a protein and its three-dimensional structure is at the very core of structural biology and bioinformatics. The occurrence and conservation of non-canonical conformations is a “local” phenomenon, i.e., non-canonical conformations are encoded intra-helically by short peptide sequences (heptapeptides at most). Effective descriptors can be formed for these short sequences employing training sets. Multiple, distinct patterns are created representing these sequences. A composite descriptor is formed by selecting from among the patterns discovered. The composite descriptor has a high level of sensitivity and specificity while, at the same time, a boosted signal-to-noise ratio.

Abstract: A crystalline structure of glutaminyl cyclase (QC) is described. Also described are the methods of preparing the crystalline structure of QC and the methods for identifying candidate inhibitors of QC. In addition, a structural basis for the rational design or identification of new inhibitors that may be used to treat QC-associated disorders is also described.

Abstract: The present invention provides a new class of peptides related to rapid replication and high human mortality, and their use in diagnosing, preventing and treating disease including vaccines and therapeutics for emerging viral diseases and methods of identifying the new class of peptides and related structures.

Abstract: A system and method of implementing a top-down flow down of at least one system requirement to allocate variability to system components such that overall system response meets the at least one system requirement, includes specifying a target value for the system response, and using a non-linear model to relate response variable values to targeted variable values and targeted mean values of the response variable values.

Abstract: A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion coefficients for the first molecular subset are first constructed via application of a translation operator to a reference set of expansion coefficients and then stored on a computer recordable medium for later retrieval. Then, a shape complementarity score, representing a correlation of the first and second molecular subsets, is computed via suitable application of rotation operators to both the stored translated expansion coefficients of the first molecular subset and the reference expansion coefficients for the second molecular subset over the sequence of different sampled configurations for the molecular combination.

Abstract: The analyst previously enters the mass of a fragment that desorbs in the first dissociation with other analysis conditions, as the precursor ion selection reference for the second dissociation through the input unit 25. When the automatic analysis is started, the controller unit 21 sequentially performs the MS1 analysis, MS2 analysis and MS3 analysis. In the course of these analyses, the data processing unit 23 determines the valence of each ion species corresponding to the peaks appearing in the mass spectrum obtained by the MS1 analysis. In addition, after the MS2 analysis, the data processing unit 23 searches for the ion species in conformity with the selection reference in consideration of the determined valence, among the ion species corresponding to the peaks appearing in the mass spectrum by the MS2 analysis. The selected ion is determined as the precursor ion for the second dissociation in the MS3 analysis.

Abstract: The present invention relates to methods, devices and systems for associating assay information with an assay consumable used in a biological assay. Provided are assay systems and associated consumables, wherein the assay system includes a reader adapted to read/erase/write information from/to an assay consumable identifier associated with the assay consumable. Various types of assay information are described, as well as methods of using such information in the conduct of an assay by an assay system.

Abstract: Techniques for protein structure analysis are provided. In one aspect, a method of analyzing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

Abstract: A method and system for monitoring a gas turbine engine (20) to predict maintenance requirements. Particles suspended in a gas flow (24, 32) of the engine (20) are monitored and quantified to predict a particle accumulation rate. Monitoring may be done using particle flow sensors (61-63) in a diverted portion (33) of the working gas flow (24), such as in the cooling gas flow (32). Particle sampling (S1-S3) may be done to determine particle size and composition distributions. Particle mass flow rates may then be continuously monitored per engine operating condition, and compared to predetermined values such as a normal upper limit per engine operating condition. An integrated particle mass flow may be used in conjunction with an instantaneous mass flow rate to predict a maintenance requirement. Multiple locations (L1-L3) may be monitored to recognize a maintenance requirement by flow section or component.

Abstract: Generally, the present invention provides a number of procedures to spatially profile proteins by using hydrophobic moments. In all procedures, a hydrophobicity distribution of a protein is shifted and normalized. In one procedure, a shape or profile of a curve of a second-order moment of hydrophobicity is determined. A second procedure involves determining one or more ratios, such as the ratio of a distance at which the second order moment of hydrophobicity vanishes to the distance at which a zero-order moment of hydrophobicity vanishes. The distance at which a peak occurs in a profile of the zero- or second-order moment of hydrophobicity can also be used for comparison. For many of these procedures, a surface or profiling contour can be chosen and used to accumulate hydrophobicities and to determine the moments. These procedures can be combined to provide a good mathematical determination of whether a protein belongs to a particular class of proteins.

Abstract: The x-ray crystal structure of BACE or BACE-like proteins is useful for solving the structure of other molecules or molecular complexes, and identifying and/or designing potential modifiers of BACE activity.

Abstract: A test method for measuring adsorbed molecular contamination uses a test structure that includes a substrate comprising a plurality of separated test sites having a plurality separate thicknesses having a base design thickness and a designed thickness interrelationship. The test structure is exposed to a molecular contaminant environment to provide an adsorbed molecular contaminant layer upon each of the plurality of separated test sites. The plurality of separated test sites with the adsorbed molecular contaminant layer thereon is measured. An appropriate algorithm that considers the designed thickness interrelationship is used to determine at least one of: (1) the base design thickness; and (2) a thickness of the adsorbed molecular contaminant layer.

Abstract: The preferred embodiments generally relate to methods and compositions that affect the GTP-binding activity of members of the Rho family GTPases, preferably Rac (Rac1, Rac2 and/or Rac3), such compositions include compounds that modulate the GTP/GDP exchange activity, along with uses for the compounds including screening for compounds which recognize Rac GTPase, and methods of treating pathological conditions associated or related to a Rho family GTPase, including Rac. The preferred embodiments also relate to methods of using such compounds, or derivatives thereof, e.g., in therapeutics, diagnostics, and as research tools.

Abstract: A data acquisition system and method are described that may be used with various spectrometers. The data acquisition system may include an ion detector, an initial processing module, and a spectra processing module. The initial processing module is provided for receiving, sampling, and processing ion detection signals received from the ion detector, and for supplying processed signals to the spectra processing module. The initial processing module includes a horizontal accumulation circuit that combines a fractional number of adjacent samples of the ion detection signals into bins. The number of adjacent samples to combine into bins may vary as a function of: (1) the time of arrival at the ion detector corresponding to that sample; (2) the mass corresponding to that sample; (3) the resolution corresponding to that sample; and/or (4) an operational mode of the spectrometer. The spectra processing module receives the processed signals and generates spectra.

Abstract: Our disclosure pertains to the field of structural biology and relates to a process to compare various three-dimensional (3D) structures and to identify functional similarities among them. Our process of comparison of 3D atomic structures is based on the comparisons of defined chemical groups onto the 3D atomic structures and allows the detection of local similarities even when neither the fold nor sequence for example aminoacid sequences for polypeptides sequences or nucleotide sequences for nucleic acid sequences are conserved. This process requires the attribution of selected physico-chemical parameters to each atom of a 3D atomic structure, then the representation of each 3D atomic structure by a graph of chemical groups.

Abstract: The invention provides methods and apparatus for characterizing complex polymeric mixture of interest. Candidate solutions are eliminated from a solution space using one or more experimental measurements of a polymeric mixture of interest. The elimination step can be repeated one or more times using different experimental measurements produced by various chemical and physical protocols, so that the remaining candidate solutions converge to describe the actual polymeric mixture under investigation. Once the composition of the complex polymeric mixture has been characterized, the information thus generated can be used to facilitate, for example, the manufacture of a bio-equivalent of the complex polymeric mixture.

Abstract: A new method is presented for measuring the molecular properties of an unfractionated solution of macromolecules. Sample aliquots spanning a range of concentrations are injected sequentially into a stream of solution and flow towards the detectors. Each aliquot produces, thereby, an effective “peak” whose elements correspond to different concentrations of the diluted aliquot. The weight averaged molar mass, the mean square radius, and the second virial coefficient of the macromolecules in solution are derived from an analysis of the angular and concentration dependence of the scattering signals throughout the corresponding peaks. In contrast to earlier on-line methods, better accuracy is achieved, while using a smaller quantity of sample. A similar method for determining cross virial coefficients between two distinct species of macromolecules is also presented.

Abstract: Fixed bond information is derived. A fixed bond representation of a chemical structure is derived from a delocalized representation. A path is conceptually traced through the represented structure and an examination is conducted, for each atom, of each possible electronic and bonding state that is consistent with what has come before along the path. A result is found by extensively or exhaustively examining all possible states and orders in a semi-recursive procedure that is directed early towards likely answers. If there is more than one possible solution, the best solution is chosen by use of a rating function.

Abstract: Systems, methods, and apparatus for propagating distilled spirit composition throughout production are disclosed. The composition of distilled spirits in each of a plurality of containers is tracked. A first distilled spirit from a first container in the plurality of containers is blended with a second distilled spirit from a second container in the plurality of containers to form a third quantity of a third distilled spirit. The third distilled spirit is placed into a third container in the plurality of containers and the composition of distilled spirits in the third container is computed based on the known composition and quantities of the first distilled spirit, the second distilled spirit, and the known composition and quantities already present in third container at a time prior to placing the first and second quantities into the third container. The composition and quantity of distilled spirits in the containers is then stored.

Abstract: Methods for using modified single wall carbon nanotubes (“SWCNTs”) to detect presence and/or concentration of a gas component, such as a halogen (e.g., Cl2), hydrogen halides (e.g., HCl), a hydrocarbon (e.g., CnH2n+2), an alcohol, an aldehyde or a ketone, to which an unmodified SWCNT is substantially non-reactive. In a first embodiment, a connected network of SWCNTs is coated with a selected polymer, such as chlorosulfonated polyethylene, hydroxypropyl cellulose, polystyrene and/or polyvinylalcohol, and change in an electrical parameter or response value (e.g., conductance, current, voltage difference or resistance) of the coated versus uncoated SWCNT networks is analyzed. In a second embodiment, the network is doped with a transition element, such as Pd, Pt, Rh, Ir, Ru, Os and/or Au, and change in an electrical parameter value is again analyzed. The parameter change value depends monotonically, not necessarily linearly, upon concentration of the gas component.

Abstract: The CrystalSym process is a logical process. It enables users of the process to easily construct symmetric systems of objects within a 3D virtual space. This process utilizes the gamut of the crystallographic 3D space filling symmetry groups of which there are 230, as well as subgroups of these 230 groups. These subgroups include point groups, line groups, frieze groups, plane groups, rod groups and layer groups. It also utilizes a certain class of non-space filling point groups.

Abstract: The present invention relates to a FabK (enoyl-acyl carrier protein reductase) protein derived from a Thermotoga maritima strain. In the present invention, the active site and the three-dimensional crystal structure of the protein are determined, a novel inhibitor against the FabK protein is screened and/or designed using the three-dimensional crystal structure thereof, and thereby developing a novel active compound, namely active-controlling material with excellent antibiotic activities against strains having a resistance to previous antibiotics.

Abstract: In a mass analysis data analyzing apparatus, centroid data is used as mass spectrum data to be analyzed. First, peaks on the centroid data are specified in order of intensity as a standard peak for identifying an isotopic cluster. The isotopic cluster is detected by comparing an emerging pattern of peaks near the standard peak and an emerging pattern of peaks of an expected isotopic cluster in the case where each valence is assumed. The valence of the determined isotopic cluster is set as the valence of the peaks belonging to the isotopic cluster, and the peak at the forefront of cluster is selected as a monoisotopic peak. With such a mass analysis data analyzing apparatus, it is possible to determine the valence of each peak and identify the monoisotopic peak in a mass spectrum.

Abstract: This disclosure provides crystalline flavonoid or flavanone isomerases, isolated non-native isomerase having the structural coordinates of said crystalline isomerase, and nucleic acids encoding such non-native isomerase. Also disclosed are methods of predicting the activity and/or substrate specificity of a putative isomerase, methods of identifying potential isomerase substrates, and methods of identifying potential isomerase inhibitors.

Abstract: A method for selecting a compound for modulating the activity of phosphoinositide dependent protein kinase 1 (PDKI) is provided. The method may comprise modelling a three dimensional structure of a plurality of molecules in a computer, comparing with the three dimensional structure of the compounds with that of a reference structure such as at least part of a protein kinase catalytic domain of PDK1, and selecting the compound based on a predicted interacting ability of the molecules to the protein kinase catalytic domain. Also a method for selecting a compound for modulating the activity of hydrophobic pocket containing protein kinase is provided. In this method, the reference structures may be one or more of a phosphate binding pocket of PDK1, a hydrophobic pocket of PDK1, and ?C helix or region interacting therewith of PDK1.

Abstract: The invention relates to a method of peptide sequencing from peptide fragment mass data, wherein a plurality of candidate peptide sequences are determined comprises the steps of: calculating peptide fragment masses, searching a plurality of peak data for masses matching said calculated peptide fragment masses, annotating all permutations of said peak data with amino acid sequences that correspond to the calculated peptide fragment masses, extending said potential sequences to resulting masses with additional matching masses, extending stepwise additions until the resulting masses correspond to parental peptide masses or said parental peptide masses minus the mass of water, and identifying at least one peptide sequence by deleting sequences that can not be extended to endpoints of said parental peptide masses, and deleting identical sequences generated.

Abstract: The present invention includes methods and apparatus for use in rapid testing for and prediction of a PPAR? response (i.e. a response similar to that of PPAR? agonists). The invention includes a PPAR? response signature comprising a set of twenty genes. The invention discloses methods whereby the differential expression of the genes of the PPAR? response signature may be used to predict whether a compound will induce a PPAR? response in a test subject.

Abstract: A method of identifying, screening, characterising or designing a chemical entity, which mimics or binds to FIH, is described. The method comprises comparing a structural model of FIH with a structural model for said chemical entity, wherein said structural model of FIH is derived from structural factors or structural coordinates determined by subjecting to X-ray diffraction measurements a crystal comprising FIH. Such chemical entities may be used in the treatment of a condition associated with increased or decreased HIF levels or activity.

Abstract: A substance analyzer utilizing Prompt Gamma Neutron Activation Analysis for identifying characteristics of a substance and method of manufacturing the same are disclosed. The analyzer is small enough to be portable and to allow its use in many applications where current analyzers cannot be utilized. The analyzer uses a neutron radiation source and a gamma-ray detector to activate the sample material and detect the prompt gamma rays emitted by the sample material. A novel housing for such an analyzer and method for making the housing are also described. Novel methods of operating such an analyzer including via a communications network are also disclosed. Also disclosed are data analysis methods that improve the accuracy and sensitivity of the results of such material analysis.

Abstract: The present invention relates to automated generation of multi-dimensional structure activity and structure property relationships.

Abstract: The present invention relates to a fuel identification system and method normally applied to internal combustion engine vehicles of the flex-fuel type by means of which it is possible to identify the composition of the fuel used at each point in time, particularly the ratio used in a gasoline/ethanol blend or detect the presence of air or fuel in the vapor state in the fuel line, using the same device that heats the fuel.

Abstract: The present invention relates to atom probe data processes and associated systems. Aspects of the invention are directed toward a computing system configured to process atom probe data that includes a data set receiving component configured to receive a first three-dimensional data set. The first three-dimensional data set has a first data element structure and is based on data collected from performing an atom probe process on a portion of an atom probe specimen. The system further includes a data set constructing component configured to create a second three-dimensional data set having a second data element structure different than the first data element structure. In selected embodiments, the system can further include a Fourier Transform component configured to perform a Fourier Transform on a portion of the second three-dimensional data set.

Abstract: The detection of protein sequence alignments firstly generates protein blocks having n successive C-alpha atoms from two protein sequences. A matrix of the distance of protein atoms from said C-alpha atoms for each block is then determined. A difference matrix is determined from respective distance matrices representing the differences between the protein blocks of the two protein structures. A Cellular Automaton (CA) model is generated in an initial configuration based upon the difference matrix, and evolved through at least one generation using predetermined rules. The rules determine which CA cells remain live and which are set to be dead.

Abstract: Methods and systems for determining information about a sample are disclosed. The methods can include measuring spectral information for the sample and determining a quantity related to a signal-to-noise ratio for the spectral information, repeating the measuring and determining until a value of the quantity is beyond a threshold value, and comparing the spectral information to reference information to determine the information about the sample.

Abstract: In one embodiment, a system or method involves accessing a database having a macromolecular structure of a protein, the molecular structure being represented as a set of spheres, retrieving the molecular structure of the protein from the database, and mathematically computing a Euclidean Voronoi diagram representing atoms of the protein from the set of spheres.

Abstract: A model of a particular biological state can be developed. The model may be used to determine if an unknown biological sample exhibits a particular biological state. This can be done by receiving either a biological sample or data associated with the biological sample. After the data is received, the data may be input into the model. In one embodiment, the acquisition of the data associated with the biological sample is performed at a first location and the imputing of the data into the model is performed at a second location different than the first location. Unless the data maps identically to the model, the data would have an inherent effect on the position of the particular clusters within the discriminatory pattern, if it is allowed to affect the model. The modeling software can keep track of the net effect on the model that each sample received has on the position of the model. If the model has drifted outside of a predetermined tolerance, the model can be updated.

Abstract: Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e.g.

Abstract: A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provisions for redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross-reactions.

Abstract: A method for predicting an amino acid sequence compatible with a three-dimensional (3D) structure of a protein. A reduced virtual representation of the 3D structure is constructed, and, for each position along the representation, its solvent accessibility is determined. For each position along the structure, an amino acid residue is randomly selected from a predefined group of amino acids having a solvent accessibility compatible with the solvent accessibility of the position. A Monte-Carlo simulation is performed on this devised protein in which an amino acid at a particular position is sequentially replaced with other amino acids having the same solvent accessibility, and an energy score is calculated for each rotamer. The lowest scoring rotamer for this position is then selected The Monte-Carlo simulation is repeated for each position along the sequence, to obtain an amino acid sequence with the lowest total energy score.

Abstract: The present invention provides the three-dimensional structure of human mitochondrial Homo sapiens peptide deformylase (HsPDF) protein, and HsPDF complexed to a binding compound, such as a PDF inhibitor. This crystallographic information will aid in the identification and development of novel binding compounds of HsPDF and other PDF family members which have anti-bacterial, anti-viral, anti-parasitical, anti-inflammatory, and/or anti-cancer activity.

Abstract: Provided are an apparatus and method of searching a protein active site. The apparatus includes a database which stores information on a plurality of reference active sites, a comparing unit which calculates 3D structural similarities according to the number of overlapping residues, with respect to an input active site and the stored reference active site, and a search unit which searches the reference active site with respect to the input active site according to the similarities. Accordingly, similar active sites can be searched with a low computational complexity, thereby be used for a correct new drug design.

Abstract: A method system, and apparatus for virtual modeling of biological tissue yields virtual multicellular individuals that exhibit adaptive emergent functionality in response to environmental stimuli. Virtual environmental parameters and cells with genomes are generated, and modified by genetic operations. Cells are developed into generations of multicellular individuals, which are evaluated and selected via evolutionary search according to fitness criteria, and individuals exhibiting adaptive emergent functionality, such as self-repair, are developed and identified.

Abstract: Provided is a method for reducing the amount of calculation time required for parameter determination, and for reducing the amount of calculation time required for parameter determination in satisfaction with a desired accuracy. The method includes preferentially selecting analysis objects, which are capable of providing parameter determination within a high degree of certainty, and controlling a calculation order of the selected analysis objects using a calculation order list.

Abstract: The present invention provides a simplified method for analyzing a structure of glycoprotein capable of conducting a peptide sequence analysis, a sugar chain sequence analysis, and an analysis of a sugar chain binding site accurately and rapidly using a mass spectrometer.

Abstract: In one embodiment, a method is disclosed that includes obtaining at least one measurement in a spectral domain of a sample and computing one or more measurements of the salient features in the spectral domain. The salient features correspond to at least one peak within the spectral domain. This method also includes classifying the computed salient features against a feature signature of nitric acid. In addition, this method includes determining if the chemical is present in the sample.

Abstract: The present invention relates to a method of identifying calcium binding sites in gamma-crystallin useful in calcium-based homeostasis for the management of Cataract, said method comprising steps of isolating gamma-crystallin from eye lens, studying binding of calcium to the isolated protein by both direct and indirect methods, identifying Greek key Motif as calcium-binding sites of the protein gamma crystallin with the said protein binding 4-mol eq of calcium having dissociation constant of 90 micromole.

Abstract: The invention relates to a device and a method for analyzing the interaction between one or more molecular species the method comprising the steps of creating streams of digital data, transferring the stream of digital data through a substrate, manipulating the molecular structure of the substrate by adding or subtracting molecules or groups of molecules to be examined to or from the substrate, receiving the streams of digital data transferred through the substrate, decoding the identity of an examined molecule or group of molecules interacting with the substrate by deciphering how the molecules affinity to another molecule or group of molecules or molecular sensor or group of molecular sensors alters the stream of digital data. The invention relates further to a method for identifying molecular species, and to a device for identifying molecular species and to a substrate for analyzing the interaction and for identifying molecular species.

Abstract: A method and a mobile terminal for gas detection warning are disclosed to solve the problem that people cannot detect gas by themselves due to the lack of a portable gas detecting apparatus. The mobile terminal is portable and typically includes a central control unit, a gas detection unit, a warning unit and a user interface unit. The apparatus performs a warning operation by using a warning policy corresponding to the detected air concentration by setting warning policies corresponding to a kind of gas in different concentration ranges respectively.