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: 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 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: 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.

Abstract: The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.

Abstract: Atomic coordinates for human serine/threonine protein phosphotase 2A (PP2A) core, as well as methods for using these atomic coordinates to prepare inhibitors of PP2A and inhibitors prepared using such methods are provided herein. A biochemical analysis of the interactions of PP2A core is also provided. Compositions including mimetics and small molecules of the invention and, optionally, secondary agents may be used to treat disorders in which PP2A activity plays a contributing role.

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: Chemical field effect sensors comprising nanotube field effect devices having biopolymers such as single stranded DNA or RNA functionally adsorbed to the nanotubes are provided. Also included are arrays comprising the sensors and methods of using the devices to detect volatile compounds.

Abstract: The present invention is directed to methods for determining electron transfer rates in systems involving metalloproteins. Metalloprotein/substrate electron transfer rates as well as metalloprotein self exchange rates may be modeled. Such electron transfer rates are useful in smart drug design and enzyme engineering.

Abstract: A method and system to blend components to form a lubricant having a predetermined characteristic. The method includes determining the characteristic from a model that relates that characteristic as a function of the amount of its components and properties of the components. These predetermined characteristics include KV (kinematic viscosities), CCS (cold cranking simulator), HTHS (high temperature, high shear viscosity), Noack Volatility, MRV (mini-rotary viscometer), Brookfield Viscosity, Soot-Dispersancy, Oxidation, Deposit, Wear, Sulfur, Phosphorus, Base Number, Color, Ash Content, Aniline Point, Acid Number, Viscosity Index, Turbidity, Demulsibility, Foam Stability, Acute Toxicity, Biodegradability, Nitrogen, and Detergency.

Abstract: A method for reproducibly analyzing mass spectra from different sample sources is provided. The method deconvolutes the complex spectra by collapsing multiple peaks of different molecular mass that originate from the same molecular fragment into a single peak. The differences in molecular mass are apparent differences caused by different charge states of the fragment and/or different metal ion adducts and/or reactant products of one or more of the charge states. The deconvoluted spectrum is compared to a library of mass spectra acquired from samples of known identity to unambiguously determine the identity of one or more components of the sample undergoing analysis.

Abstract: A System and Method for Gas Recognition by Analysis of Bispectrum Functions is based on the Higher-Order Spectral analysis of time series measurements of resistance fluctuations in Metal Oxide Semiconductor (MOS) gas sensors, such as Taguchi-type sensors. A two-dimensional contour plot module of the bispectrum function is treated as a pattern. These patterns include information about the analyte(s) whereby characteristics of the gas can be identified.

Abstract: Systems and methods for computing three-dimensional (3D) Euclidean Voronoi diagrams are disclosed. For some embodiments, a set of 3D objects is accessed, in which each 3D object is mathematically defined. Thereafter, a Voronoi region associated with each of the 3D objects is computed, thereby resulting in a complete Euclidean Voronoi diagram of the set of 3D objects. In some embodiments, the 3D objects are spheres, each of which is defined by a center and a radius. For other embodiments, the 3D objects are convex objects, each of which is mathematically-definable (e.g., cylinders, sphero-cylinders, etc.). Unlike prior approaches that suggested using a numerical approach to computing the Voronoi diagram, the present disclosure employs mathematical approaches for computing the Euclidean Voronoi diagram, thereby improving efficiency in the computation of the Euclidean Voronoi diagram.

Abstract: The invention aims to provide a highly accurate automatic biopolymer determination technique utilizing mass spectrometry whereby calibration prior to measurement or the addition of an internal standard to a sample can be eliminated. The biopolymer automatic identifying method of the invention comprises: retrieving a candidate molecule by matching an observed mass value X obtained by mass spectrometry with a predetermined database; selecting an arbitrary number of candidate molecules with high similarity scores; calibrating the observed mass value X using the candidate molecule as an internal standard; calculating relative error Ec between a calibrated mass value Xc and a theoretical mass value M of the candidate molecule; determining the standard deviation SEc of the relative error; determining a tolerance Tc of database search from the standard deviation SEc; and repeating a database search based on the tolerance Tc.

Abstract: Embodiments of the present invention relate to the identification of proteins using laser desorption ionization mass spectrometry, the identification of source organisms comprising the identified proteins and a computer readable storage medium storing instructions that, when executed by a computer cause the computer to perform a method for the identification of proteins using mass spectra generated through the application of laser desorption ionization mass spectrometry of the proteins.

Abstract: A method, computer system, and computer program product for determining N disulphide bond connections in a protein having 2N bonded sulphur atoms. Each sulphur atom is available for forming the N disulphide bond connections through use of an undirected graph having the 2N sulphur atoms as nodes and having an edge connecting each pair of nodes. Each sulphur atom is comprised by a cysteine of the protein. The cysteines are sequenced along a chain in the protein as ordered list of position indexes. A weight W of each edge between cysteine position indexes I1 and I2 is calculated as decreasing with increasing separation d between I1 and I2, wherein d is |I1?I2|/100. The N disulphide bond connections are determined by optimizing an objective function formed from the calculated weights W.

Abstract: The virtual screening of a database of molecules is based on explicit three-dimensional molecular superpositions. The torsional flexibility of the database molecules is taken fully into account, and an arbitrary number of conformation-dependent molecular features may be considered. A fragmentation-reassembly approach is utilized, which allows for an efficient sampling of the conformational space. A fast clique-based pattern-matching algorithm generates alignments of pairs of adjacent molecular fragments on the (rigid) query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups), it is possible to rapidly produce accurate alignments of medium-sized drug-like molecules. Examples with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) show that average query processing times of the order of 0.

Abstract: A method to be implemented on or in a computer is disclosed, where the method includes data collection, calibration, candidate selection, and analysis of data streams associated with each candidate to classify single molecule fluorescence resonance energy transfer events. Once classified, the classification can be related to the nature of the events, such as the identification of dNTP incorporation during primer extension to obtain a base read out of an unknown template.

Abstract: Sample analysis apparatuses are disclosed that can include processing circuitry configured to acquire one data set from an analysis component configured according to one analysis parameter set, and prepare another analysis parameter set using another previously acquired data set. Sample analysis methods are also disclosed that can include acquiring first and second data sets from an analysis component and using the process and control component to process the first data set to prepare a second analysis component parameter set. Sample analysis instruments are disclosed that can include processing circuitry coupled to a storage device with the storage device including analysis component parameter sets associated with data parameter values with individual ones of the analysis component parameter sets being associated with individual ones of the data parameter values.

Abstract: The invention relates to a method for determining the isomer composition in an isocyanate isomer mixture, wherein a spectrum of the isomer mixture is recorded and the spectrum is entered into a chemometric calibration model.

Abstract: This invention provides methods of identifying an Eg5 binding ligand. The ligand is identified by using the atomic coordinates of an Eg5 crystal to generate a three dimensional structure. The three dimensional structure is used in molecular modeling techniques and docking experiments to identify ligands that bind to the binding pocket of Eg5. A novel binding pocket is identified. The invention also provides a crystallized Eg5 and ligand complex.

Abstract: A method for designing a metal ion for use in a molecular dynamics simulation can include the steps of building a metal ion molecule having a center atom and a dummy atom, assigning a van der Waals radius to the center atom, and assigning a charge to the dummy atom. A metal ion molecule may have the center atom covalently linked to one or more dummy atoms resulting in the metal ion molecule having a polyhedron geometry. New force field parameters may be used in methods for designing metal ions for use in molecular dynamics simulations.

Abstract: A computer facilitated method of requesting a spectral analysis of a sample having an unknown concentration or purity, performing an energy absorption analysis of the sample to obtain spectral data regarding the analysis and comparing the spectral data to a stored spectral data regarding the analyses of the samples having a predetermined concentration and purity to determine the concentration or purity of the sample having an unknown concentration or purity. The spectral analysis is performed on site where the sample is prepared or administered using a portable analytical apparatus and provides a real time report of the concentration or purity of the sample. The apparatus requires only a small sample size.

Abstract: The present invention provides a means of economically, quickly and efficiently designing a physiologically active peptide to a target protein. Specifically, the present invention provides a method of designing a physiologically active peptide characterized in that, to design a physiologically active peptide capable of binding to a target site comprising a consecutive or non-consecutive amino acid sequence in a target protein, a computerized processing is carried out for extracting a preferable amino acid sequence by calculating intermolecular energy etc.; an apparatus therefor; a program for executing the above-described processing by a computer; and a computer-readable recording medium containing the program.

Abstract: The crystal structures of catalytic domain of HPTPbeta, both ligand-bound and ligand-free are described. These structures are useful in computer aided drug design for identifying compounds that bind or activate HPTPbeta and thereby modulate angiogenesis mediated disorders or diseases.

Abstract: The extracellular loop of CD81 is a cellular receptor for the E2 protein of hepatitis C virus. A CD81 crystal structure has been elucidated and is provided for use in the structure-based design of compounds which bind to CD81 and thus block the binding of HCV. Methods such as docking and de novodrug design can be used.

Abstract: Method of identifying compounds that modulate intermolecular interactions between a target protein and a modifier are disclosed. Pharmaceutical composition comprising compounds that inhibit intermolecular interactions between a target protein and a modifier are disclosed. Methods of treating individual suffering from inflammatory conditions, undesirable immune responses, immunological conditions and bacterial infections are disclosed.

Abstract: A method includes: accumulating ions having a plurality of m/z values in an ion trap during a time interval; deriving from the accumulated ions a respective intensity value for each of the m/z values; and adjusting each of the intensity values as a function of the time needed by the ion trap to begin collecting ions with the corresponding m/z value. According to a different aspect, an apparatus includes a first portion with an ion trap, and a second portion. The second portion causes the ion trap to accumulate ions with a plurality of m/z values during a time interval, derives from the accumulated ions in the ion trap a respective intensity value for each of the m/z values, and adjusts each of the intensity values as a function of the time needed by the ion trap to begin collecting ions with the corresponding m/z value.

Abstract: The present invention relates to a space-invariant independent component analysis and electronic nose for detection of selective chemicals in an unknown environment, and more specifically, an approach to analysis of sensor responses to mixtures of unknown chemicals by an electronic nose in an open and changing environment. It is intended to fill the gap between an alarm, which has little or no ability to distinguish among chemical compounds causing a response, and an analytical instrument, which can distinguish all compounds present but with no real-time or continuous event monitoring ability.

Abstract: A surface analysis apparatus includes a unit configured to bombard a sample surface with at least two types of ions having different sizes; a measurement device for measuring, with a time-of-flight secondary ion mass spectrometer, a mass spectrum of ions emitted from the sample surface; and an information processor outputting a difference between two mass spectra measured by bombardment of different types of ions.

Abstract: A method and computer program product for simulating a pan coating process estimates at least one of tablet coating uniformity or coated tablet weight uniformity for tablets within a tablet bed of a pan. The simulation includes obtaining a plurality of parameters associated with the pan coating process, selecting tablet paths for each cycle of a simulation tablet in the tablet bed, determining a coating amounts for the tablet based on selected tablet paths, determining cycle times for the tablet, and summing the determined coating amounts and cycle times for the tablet. The simulation is repeated for each of a defined number of simulation tablets representing the tablets within the tablet bed to determine tablet coating uniformity and/or coated tablet weight uniformity for the tablets. Tablet paths and/or cycle times are determined randomly, e.g., in accordance with a Monte Carlo method.

Abstract: The present invention is directed to a nucleic acid quantification kit and method for determining the initial concentration or mass fraction of a target nucleic acid present in a sample. Illustrative embodiments include real-time competitive quantitative polymerase chain reaction (PCR) to determine the copy number or mass fraction of a target nucleic acid sequence in a sample and use of a thermodynamically based signal processing algorithm, with or without PCR, to provide mass fraction information.

Abstract: This invention is directed to the three dimensional crystal structure of Beta-site APP Cleaving Enzyme (BACE), and to the use of this structure in rational drug design methods to identify agents that may interact with active sites of BACE. Such agents may represent new therapeutics in the treatment and/or prevention of Alzheimer's Disease.

Abstract: When a liquid mixture of two samples such as biological samples labeled with stable isotopes is subjected to a relative quantitative analysis using a liquid chromatography-tandem mass spectrometry system, various constituents are simultaneously ionized. Accordingly, sufficient time required for second mass spectrometry is not ensured, whereby some ions remain unanalyzed after measurement. To address this problem, after second mass spectrometry, amino acid sequencing is performed using the analysis data of the second mass spectrometry, which enables determination on the presence/absence of a specific amino acid labeled with a stable isotope. When the specific amino acid is present, the m/z value of an isotopically-labeled-paired ion in an MS spectrum is calculated, and non-target information for use in second mass spectrometry is created using the calculated m/z information.

Abstract: Methods and systems for determining if one or more target molecules are present in a gas, by exposing a functionalized carbon nanostructure (CNS) to the gas and measuring an electrical parameter value EPV(n) associated with each of N CNS sub-arrays. In a first embodiment, a most-probable concentration value C(opt) is estimated, and an error value, depending upon differences between the measured values EPV(n) and corresponding values EPV(n;C(opt)) is computed. If the error value is less than a first error threshold value, the system interprets this as indicating that the target molecule is present in a concentration C?C(opt). A second embodiment uses extensive statistical and vector space analysis to estimate target molecule concentration.

Abstract: Embodiments of the present invention relate to atomic coordinates for PME-1 alone or in complex with PP2A, as well as methods for using these atomic coordinates to prepare inhibitors of PME-1 and/or PP2A and inhibitors prepared using such methods. Further embodiments relate to biochemical analyses of the interactions of PME-1 alone or in complex with PP2A. Further embodiments relate to compositions including mimetics and small molecules, optionally, secondary agents, which may be used to treat disorders in which PME-1 and/or PP2A activity plays a contributing role.

Abstract: The present invention relates to the use of simulation technology to rationally optimize the locations and sizes of attached polymeric moieties for modification of therapeutic proteins and the proteins generated from this method.

Abstract: The invention relates to crystals of the influenza virus neuraminidase protein, their structures and their use.

Abstract: The invention provides an X-ray crystal structure of the 30S ribosome, obtained from Thermus thermophilus 30S subunit, having a tetragonal space group P41212 with unit cell dimensions of a=401.4±4.0 ?, b=401.4±4.0 ?, c=175.9±5.0 ?. An advantageous feature of the structure is that it diffracts beyond 3 ? resolution. The invention also provides a crystal of 30S having the three dimensional atomic coordinates of the 30S ribosome, the coordinates being provided in Tables 1A and 1B. The data may be used for the rational design and modelling of inhibitors for the 30S ribosome, which have potential use as antibiotics.

Abstract: A method for the orthogonalization of initially overlapping vectors, the uses for which include the re-encoding and decoding of representations triggered by sensory arrays.

Abstract: A conformation analysis device and analysis method with which discrimination can be achieved even if there is a subtle difference in a conformational structure, a given molecule can be processed in a unified manner, and large-scale computer processing can be performed, and a conformational notation device and notation method with which even in the case where a conformation cannot be uniquely determined if a rule in accordance with the IUPAC Nomenclature is followed, the conformation can be uniquely notated, a given molecule can be processed in a unified manner, and large-scale computer processing can be performed, are provided.

Abstract: A method for separating detection channels is disclosed, a sample (15) being equipped with at least two different fluorescent dyes. Firstly the emission spectrum of at least two fluorescent dyes is ascertained. From the emission spectra, the separation points of the wavelength and of the individual detection channels are determined. Lastly, adjustment of the separation of the at least two channels is accomplished on that basis.

Abstract: Crystalline IGF-1 is provided along with a method for production thereof. Crystallizing IGF-1 comprises the steps of mixing an aqueous solution comprising IGF-1 with a reservoir solution comprising a precipitant to form a mixture; and crystallizing the mixture, optionally also recrystallizing and isolating the crystalline IGF-1. In addition, a method for identifying IGF-1 indirect agonists is provided using a detergent as a standard for the level of inhibition of binding of IGFBP-1 or IGFBP-3 to IGF-1 and/or using the coordinates of the binding pockets of IGF-1 to which a candidate indirect agonist binds for structure-based drug design.

Abstract: In one aspect of the present invention, the less “useful” spectral data is disregarded from the spectral data resulting from the fragmentation by ETD and candidate charge states for the “useful” data assigned. Knowledge of the first order ion product charge state reduces the subset of comparison data hence aiding in the eventual identification of the precursor ion, and thus aiding in peptide sequence database searching capabilities. Such capabilities include, but are not limited to, computational requirements for database search and data storage, CPU time, the volume taken up on the hard disk to store results, visualization and dissemination of data, and overall improvement in the confidence in the precursor identification. Thus determination of the peptide sequence can be resolved in less time, costing less money, and requiring less computer power.

Abstract: The present invention relates to X-ray crystallography studies of a human Janus Kinase 2 (JAK2) domain. More particularly, it relates to the crystal structure of a JAK2 kinase domain bound to a inhibitor. The invention further relates to the use of the crystal and related structural information to select and screen for compounds that interact with JAK2 and related proteins and to compounds that could be used for the treatment of diseases mediated by inappropriate JAK2 activity.