70 results about "Atomic coordinates" patented technology

The present invention provides a fluorescent substance excellent both in quantum efficiency and in temperature characteristics, and also provides a light-emitting device utilizing the fluorescent substance. This fluorescent substance contains an inorganic compound comprising a metal element M, a trivalent element M¹ other than the metal element M, a tetravalent element M² other than the metal element M, and either or both of O and N. In the inorganic compound, the metal element M is partly replaced with a luminescence center element R. The crystal structure of the fluorescent substance is basically the same as Sr₃Al₃Si₁₃O₂N₂₁, but the chemical bond lengths of M¹-N and M²-N are within the range of ±15% based on those of Al—N and Si—N calculated from the lattice constants and atomic coordinates of Sr₃Al₃Si₁₃O₂N₂₁, respectively. The fluorescent substance emits luminescence having a peak in the range of 490 to 580 nm when excited with light of 250 to 500 nm.

A method of simulating a molecular system using a hybrid computer is provided. The hybrid computer comprises a classical computer and a quantum computer. The method uses atomic coordinates {right arrow over (R)}_n and atomic charges Z_n of a molecular system to compute a ground state energy of the molecular system using the quantum computer. The ground state energy is returned to the classical computer and the atomic coordinates are geometrically optimized on the classical computer based on information about the returned ground state energy of the atomic coordinates in order to produce a new set of atomic coordinates {right arrow over (R)}′_n for the molecular system. These steps are optionally repeated in accordance with a refinement algorithm until a predetermined termination condition is achieved

This invention provides modified, insecticidal Cry35 proteins with enhanced properties as compared to wild-type Cry35 proteins. The modifications to these proteins were based in part on analysis of the atomic coordinates and three-dimensional (3D) structure of the ˜45 kDa 149B1 protein and other proteins in the Cry35 class. The subject invention also includes polynucleotides that encode these modified proteins, and transgenic plants that produce these modified proteins. This invention further provides methods of controlling plant pests, including rootworms, with these modified proteins. The modified proteins of the subject invention include chimeric toxins involving exchanged segments, domains, and motifs as discussed herein. The subject invention also provides methods of modifying Cry35 proteins.

The invention discloses a method for building a multiphase polycrystalline atomic structure model. The method includes the following steps: 1. preparing an atomic coordinate file of super cell structures of all phases of the built structure; 2. obtaining vertex coordinates of convex polyhedrons of a plurality of crystalline grains of any sizes through Qhull software; 3. rotating the coordinates of a supper cell of a phase at any angle, and through a method for judging inner and outer points of a polyhedron, selecting atomic coordinates of the phase inside the crystalline grain; and determining atomic coordinates of any phase inside any crystalline grain by using the same method; and 4. by controlling the proportion of all phases that fill the crystalline grains, a coordinate file of the multiphase polycrystalline atomic structure model of any phase number, any phase proportion and any crystalline grain size can be obtained by using the step 3. The method in the invention is easy to operate, has relatively low requirements for software and hardware of a computer, and can build a multiphase polycrystalline atomic structure model of a relatively large structure.

This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

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 Å, b=401.4±4.0 Å, c=175.9±5.0 Å. An advantageous feature of the structure is that it diffracts beyond 3 Å 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.

The invention belongs to the technical fields of computational chemistry and physics and particularly relates to a complicated function minimal value searching method based on a constrained regular pattern. In the complicated function minimal value searching method, an atomic coordinate corresponding to an energy minimal value is solved by virtue of the input atomic coordinate, a known potential energy surface energy function and a first-order derivative of the energy function corresponding to the coordinate. The method comprises the steps: starting from a coordinate system corresponding to one minimal value, carrying out optional generating and analyzing to obtain one constrained regular pattern, realizing a purpose of surpassing an energy maximal value of the potential energy surface by continuously adding bias potential functions and repeating optimizing of the energy minimal value, and finally obtaining the coordinate system corresponding to a new minimal value. The complicated function minimal value searching method based on the constrained regular pattern has the effect that the overall minimal values can be quickly searched, is suitable for complicated function systems, and meanwhile has a function of searching an optimal reaction channel. The complicated function minimal value searching method based on the constrained regular pattern can be used for traversing the potential energy surfaces of complicated molecules and periodic crystal systems.

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 Å, b=401.4±4.0 Å, c=175.9±5.0 Å. An advantageous feature of the structure is that it diffracts beyond 3 Å 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.

A self-organizing method, system, and computer program product for generating molecular conformations that are consistent with a set of distance and/or volume constraints. A stochastic proximity embedding (SPE) algorithm evaluates individual distance and/or volume constraints and adjusts the atomic coordinates to minimize violations of such constraints. The method scales linearly with thenumber of atoms, and produces many more unique conformations at a fraction of the time required by conventional distance geometry algorithms.

Atomic coordinates for human phosphotyrosyl phosphatase activator (PTPA) and ATPγS bound by PTPA, as well as methods for using these atomic coordinates to prepare ATPase inhibitors of PTPA and ATPase inhibitors prepared using such methods are provided herein. Comprehensive biochemical analyses of the interactions of PTPA with ATP and protein phosphatase 2A are also provided. Compositions including mimetics and small molecules of the invention and, optionally, secondary agents may be used to treat disorders in which PTPA ATPase activity plays a contributing role.

The crystal structure at 2.16 Å resolution of the full-length bacterial bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli, in complex with its inhibitor moenomycin, is provided. The atomic coordinates of the complex as well as the moenomycin binding site are provided. Three dimensional structures of amino acid residues involved in moenomycin binding and transglycosylation activity are identified. Binding site for peptidoglycan synthesis inhibitors comprising inhibitor-binding site comprises amino acid residues from at least one of transglycosylase (TG), UvrB domain 2 homolog (UB2H) and transmembrane (TM) domains of PBP1b are identified at an atomic level of resolution. Methods for rational drug design based on the atomic coordinates are provided. Methods for screening for antibiotics based on anisotropic binding assay and transglycosylase inhibitor assays are provided. Novel antibiotics based on the screening assays of the invention are disclosed.

Crystals and structures are provided for an eukaryotic RNA polymerase, and an elongation complex containing a eukaryotic RNA polymerase. The structures and structural coordinates are useful in structural homology deduction, in developing and screening agents that affect the activity of eukaryotic RNA polymerase, and in designing modified forms of eukaryotic RNA polymerase. The structure information may be provided in a computer readable form, e.g. as a database of atomic coordinates, or as a three-dimensional model. The structures are useful, for example, in modeling interactions of the enzyme with DNA, RNA, transcription factors, nucleotides, etc. The structures are also used to identify molecules that bind to or otherwise interact with structural elements in the polymerase.

The invention discloses a crystal space structure transformation method and system. The method comprises the following steps: reading a crystal file, converting cell parameters, intramolecular atomiccoordinates and space group information in the file into an object-oriented data structure for storage, and converting the object-oriented data structure into a new object data structure, copying cellattributes and space group attributes in a crystal structure in the object-oriented data structure to corresponding attributes in a new crystal structure, reading position information of all atoms ina molecule in the molecular structure, and determining an atomic chain of each atom according to the position information of the atoms; calculating crystal lattice energy, and adjusting cell attribute parameters and flexible bond values according to a set step length; and converting the new object data structure into an object-oriented data structure, and storing the object-oriented data structure. According to the method and the system, the parameter space of the crystal is converted from describing the fractional coordinate of each atom in the crystal cell into describing the relative position between two adjacent atoms in the crystal through conversion, so that the whole parameter space is continuously changed in the crystal evolution process.

A composition-of-matter comprising a crystallized form of a large ribosomal (50S) subunit of a pathogenic bacterium, and the atomic coordinates of the three-dimensional structure thereof are provided herein, as well as methods for crystallizing the same, and using the atomic coordinates of the same to design de novo ligands with high specificity thereto.

A WW domain crystal structure of Pin1 is provided. In addition, methods of using the crystal structure and atomic coordinates for the development of WW domain binding agents is also provided. Also provided are computer programs on computer readable medium for use in developing WW domain binding agents.

A computer-readable storage medium encoded with computer-readable program code for causing a computer to perform a molecular dynamics simulation for determining the solvent accessible surface area of a molecule (M) with respect to atomic coordinates, wherein the molecule (M) comprises a plurality of atoms, a sphere (B_i) is assigned to each atom, and each sphere (B_i) comprises a radius (ρ_i) and a center position (r_i). The program code includes instructions for: determining for each sphere (B) all neighbouring spheres (B_i) that intersect with the sphere (B); defining a set of one or more contours (C_m), such that all intersecting circles of sphere B with spheres B_i intersect on the surface of sphere B; determining for each contour (C_m) an area enclosed by the contour (C_m), wherein the contour (C_m) includes the area on the surface of said sphere (B) that is enclosed by one or more arcs (a₁, a₂, a₃) resulting from an intersection of the surface of said sphere (B) with one of the surface of one intersecting sphere (B_i) or the surfaces of a plurality of intersecting spheres (B_i) that have an overlapping intersection area on the surface of said sphere (B); determining the solvent accessible surface (S) of said sphere (B) as the surface of said sphere (B) subtracted by the area comprised by all contours (C_m) on the surface of said sphere (B); and determining the solvent accessible surface area of the molecule (M) based on a sum of solvent accessible surface areas (S_i) of the spheres.

The invention discloses a calculation method and device for an atom close-packed surface and a two-dimensional dot matrix, and belongs to the technical field of material structure characterization and modeling calculation. The method comprises the following steps of: establishing a supercell expanded on the basis of an originally input atomic dot matrix; obtaining atom combinations capable of forming a plane in primitive cells based on an originally input atom dot matrix; judging whether each atom in the expanded supercell and each surface in the primitive cell are coplanar or not; and obtaining the distribution conditions of several atom combinations with the maximum coplane atom number and the atom dot matrix in all atom combinations in the supercell. According to the method, the atomic coordinates of at least one surface with the maximum number of atoms in the same plane and/or close to the maximum number of atoms and the corresponding coplanar atom coordinates in the supercell can be calculated, and the method is suitable for crystal structures except cubic crystals and hexagonal crystals; and a novel mode which is wide in applicability, simple and rapid is provided for obtaining the atom close-packed surface and the two-dimensional dot matrix of the crystal material.

This disclosure relates to a process for manufacturing a mono-alkylaromatic aromatic compound, said process comprising contacting a feedstock comprising an alkylatable aromatic compound and an alkylating agent under alkylation reaction conditions with a catalyst comprising EMM-13, wherein said EMM-13 is a molecular sieve comprising a framework of tetrahedral atoms bridged by oxygen atoms, the tetrahedral atom framework being defined by a unit cell with atomic coordinates in nanometers shown in Table 3.

This invention relates to a process for using computerized molecular interaction modeling to predict the adhesive interactions between a substrate and a polymer. The molecular modeling method may be used to predict and select optimal adhesion promoting monomers for use in latex polymer coatings, providing the best wet adhesion to alkyd-coated substrates. The molecular modeling method could also predict substrate polymer pairs having the least affinity, and thus the most useful as a release liner. The method involves the steps of:

• • a) identifying interacting chemical segments on both the surface and the polymer;
  • b) generating models of the interacting segments, said models describing the spatial relationship of each atom in the segment and the connectivity between the atoms;
  • c) merging the models of each surface segment with each polymer segment to describe each possible interacting surface/polymer pair;
  • d) generating several hundred random configurations for each surface/polymer pair merged models, by choosing random values for the six spatial variables, that describe the relative orientations of two objects;
  • e) optimizing the atomic coordinates of each surface/polymer segment interaction model by calculating the minimum of the molecular potential energy;
  • f) computing the pair interaction energy for each merged model pair;
  • g) averaging the pair interaction energies; and
  • h) comparing the average pair interaction energies of each surface/polymer pair to choose the best pair for the intended application.