Collaborative Computational Project Number 14
for Single Crystal and Powder Diffraction
CCP14
Software Patents (and other Patents) Involving Crystallography
(Mainly trying to find relevant Software Patents - and other crystallographic patents that caught my eye)
The CCP14 Homepage is at http://www.ccp14.ac.uk
[CCP14 Maths and Algorithms Page] | [Software Patents and Crystallography Homepage] | [Patents Involving Crystallography] | [Software Patent Links and Resources] | [The potential power of 'Software Patents' to destroy Crystallographic Software]
Searching the US Patent Full-Text and Full-Page Image Databases : http://www.uspto.gov/patft/index.html
Searching the US Issued Patent Full-Text and Full-Page Image Databases : http://patft.uspto.gov/netahtml/search-bool.html
Searching the US Patent Applications Full-Text and Full-Page Image Databases : http://appft1.uspto.gov/netahtml/PTO/search-bool.html
"Manual of Patent Examining Procedure" - 1900 Protest: http://www.uspto.gov/web/offices/pac/mpep/documents/1900.htm
Searching European patent information : http://www.european-patent-office.org/espacenet/info/access.htm
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If the following links do not work (due to them being part of a boolean search) - just go to the above search page and type in the patent number.
Also, there might be some duplication due to using different Patent databases as well as different search techniques.
US Patent system last checked 27th September 2002
US Patent Number: 5,249,137
US Patent Title: Computer-aided chemical illustration system
Date of Patent: September 28, 1993
Abstract: A computer-aided chemical illustration system is disclosed. Techniques provided include: 1) efficient drawing of bonds; 2) drawing different bond types during a single mode; 3) determining bisect angles for bonds; 4) labeling atoms on the fly; 5) automatic alignment of atom labels; 6) custom alignment of atom labels; 7) changing the type, style, or orientation of an object while it is being drawn; 8) detection of ring structures; and 9) shifting bonds around on a ring.
US Patent Number: 6,582,233
Patent Title: Apparatus and method for monitoring the validity of a molecular model
Date of Patent: June 24, 2003
Abstract: A computer implemented molecular modeler displays information concerning structural validity to the user. The display of information may be updated substantially continuously while the user modifies the molecular model. The display of information may comprise a color coded indicator and/or text associated with the atoms of the molecular model.
US / European / World Patent Number/ Request: WO9906824
Patent Title: Method and apparatus for determining molecular crystal structures
Publication Date: 1999-02-11
Abstract: An improved method and apparatus for determining molecular crystal structures is provided which enables molecular crystal structures to be identified using only powder diffraction data, that is considerably faster than conventional crystal modelling techniques. With the improved crystal modelling method and apparatus trial molecular crystal structures are reduced to a unique set of variables based on co-ordinates representative of the location and orintation of the molecule and where appropriate at least one co-ordinate representative of a torsion angle, bond length or bond angle. In addition, the total quantity of experimental powder diffraction data is reduced to provide a reduced representation of the diffraction data in the form of a structure factor intensity listing and covariance matrix. Trial crystal structures are postulated and each is defined using the set of variables which are used in determining a fitness of each trial structure with respect to the reduced representation of the experimental data. A trial crystal structure is output as an accurate representation of the actual crystal structure, when the fitness value for the trial structure is less than or equal to a predetermined threshold value. With the improved crystal modelling method and apparatus, identification of complex molecular crystal structures can be performed in seconds or minutes using the current generation of conventional personal computers or workstations as opposed to the hours and often days required with conventional techniques.
European Patent Number: EP0526516
World Patent Number: WO 91/16682
Patent Title: Handling Data
Date of Patent: 1991-10-30
Abstract: A method of structuring or storing data within a file has the following steps: (i) arranging the file into a plurality of data blocks each preceded by a respective data block code; and (ii) arranging the data within each block into a plurality of data items each preceded by a respective data name; wherein the data block codes are taken from a first predetermined set, may occur in any order, and have a first common feature, and wherein the data names are taken from a second predetermined set, may occur in any order, and have a second common feature, the first and second common features being readily distinguishable. The file is visually readable as text in addition to being machine readable
United States Patent Application: 20020107643
Patent Title: Process for pan-genomic determination of macromolecular atomic structures
August 8, 2002
Abstract: A process for pan-genomic determination of three-dimensional macromolecular atomic structures uses a unique combination of components. All known structural information, sequence information and functional information are systematically organized into a genomics database. Advanced tools of bioinformatics are used to cluster all known gene products into families of homologous sequences. Simultaneously, in parallel for each such family, a few cDNAs from appropriately representatives species are cloned into expression vectors for a few expressions systems. Constructs are then screened for expression, and those that are effective advance to the preparative step. Expressed proteins are prepared, purified and characterized. Purified proteins are set to crystallize in parallel against crystallization screens. Crystals that grow are tested for suitable diffraction characteristics. A suitable crystal is frozen, and diffraction data are measured using the multiwavelength anomalous diffraction (MAD) method at a synchrotron which uses undulator beamlines for high-throughput crystallography. Diffraction data are analyzed by the MAD phasing method, an atomic model is built, and the model is refined against the diffraction data. The refined model is analyzed in the context of (1) sequence information from other family members, (2) all other known 3D structures, and (3) functional motifs. It is also analyzed for surface characteristics with the aim to define active sites and macromolecular contact sites. For relevant structures, the active site properties are used to define classes of compounds predicted to have binding potency. Computational tools for homology model building are used to develop models for homologs. The homology models may be used in target selection, drug design, or design of more appropriate constructs for experimental analysis. The ensemble of all known structures is used to further advance the effectiveness of the bioinformatics tools.
US Patent Number: 6,411,676
Patent Number: US6411676
Patent Application Number: EP1075653 (WO9956115)
Patent Title: Method for determining parameters of a unit cell of a crystal structure using diffraction
Publication Date: 2002-06-25
Abstract: A method for determining the parameters of a unit cell of a crystal structure using diffraction is presented. The method includes the steps of repeatedly rotating the crystal at a predetermined angle, while the crystal moves in relation to a detection surface and measuring the position of radiation reflected from the crystal. The resulting combined measurements are utilized to accurately determine the unit cell dimension and orientation of the crystal
EPO Patent Application: EP1260812
Patent Title: Process and apparatus for the x-ray diffraction characterization of a material with amorphous phase
Date of Patent: March 6, 2001
Abstract: The invention relates to a process for the qualitative and quantitative characterisation of a material (2) containing at least one amorphous portions by analysis of X-ray diffraction pattern in which a combined diffraction pattern of the material and of a crystalline Standard is analyzed with Rietveld method in a computerized device. According to the invention, the combined diffraction pattern (11) is obtained by the linear mathematical combination of a measured diffraction pattern of the material to be analyzed. An apparatus for working the process is also claimed.
US Patent Number: 6,198,796
Patent Title: Method and apparatus of automatically selecting bragg reflections, method and system of automatically determining crystallographic orientation
Date of Patent: March 6, 2001
Abstract: A novel method and novel apparatus that are capable of selecting, with a computer, reference Bragg reflections pc1 and pc2, which form a basis for determination of the crystallographic orientation of a crystal sample by the two-reflection method, automatically and easily and accurately, wherein; firstly, x-ray intensities and diffraction conditions of all Bragg reflections which are measurable are calculated using the crystallographic information, secondly, a weight-point according to both the x-ray intensity and the angle between the sample normal and the scattering vector is obtained for each of the Bragg reflections, thirdly, two Bragg reflections having the two largest weight-points are selected as the reference Bragg reflections pc1 and pc2, respectively.
United States Patent Application: 20020116133
United States Patent Application Title: Method for removing atomic-model bias in macromolecular crystallography
Date of Patent: August 22, 2002
Abstract: Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.
World Patent Number: WO0190715
Patent Title: Maximum likelihood density modification by pattern recognition of structural motifs
Date of Publication: 2001-11-29
Abstract: An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F(sub)h(end sub)} using a local log-likelihood function: LL((rho)(x,{F(sub)h(end sub)})) = 1n p((rho)(x. PROT)p(sub)PROT(end sub)(x) + p((rho)(x) . SOLV)p(sub)SOLV(end sub)(x) + p((rho)(x). H)p(sub)H(end sub)(x) , where .(sub)PROT(end sub)(x) is the probability that x is in the protein regions, p((rho)(x).PROT) is the conditional probability for (rho)(x) given that x is in the protein region, and p(sub)SOLV(end sub)(x) and p((rho)(x).SOLV) are the corresponding quantities for the solvent region, p(sub)H(end sub)(x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; andp ((rho)(x).H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.
US Patent Number: 6,438,205
Patent Title: System and method for reducing phase ambiguity of crystal structure factors
Date of Patent: August 20, 2002
Abstract: A method reduces the structure factor phase ambiguity corresponding to a selected reciprocal lattice vector. The method includes generating an original phase probability distribution corresponding to a selected structure factor phase of the selected reciprocal lattice vector. The original phase probability distribution includes a first structure factor phase ambiguity. The method further includes combining the original phase probability distribution with a plurality of phase probability distributions of a plurality of structure factor phases of other reciprocal lattice vectors using a phase equation or inequality. The phase equation or inequality defines a mathematical relationship between the selected structure factor phase of the selected reciprocal lattice vector and the plurality of structure factor phases of other reciprocal lattice vectors. The method further includes producing a resultant phase probability distribution for the selected structure factor phase of the selected reciprocal lattice vector. The resultant phase probability distribution includes a second structure factor phase ambiguity which is smaller than the first structure factor phase ambiguity.
Lachlan's Note: Looks defined for powder diffraction??
US Patent Number: 6,438,204
Patent Title: Linear prediction of structure factors in x-ray crystallography
Date of Patent: August 20, 2002
Abstract: A method uses linear prediction analysis to define a first structure factor component for a first reflection from x-ray crystallography data. The x-ray crystallography data includes a set of cognizable reflections. The method includes expressing the first structure factor component as a first linear equation in which the first structure factor component is equal to a sum of a first plurality of terms. Each term includes a product of (1) a structure factor component for a cognizable reflection from the x-ray crystallography data, wherein the cognizable reflection has a separation in reciprocal space from the first reflection, and (2) a linear prediction coefficient corresponding to the separation between the cognizable reflection and the first reflection. The method further includes calculating values for the linear prediction coefficients. The method further includes substituting the values for the linear prediction coefficients into the first linear equation, thereby defining the first structure factor component for the first reflection.
US Patent Number: 6,345,235
Patent Title: Method and apparatus for determining multi-dimensional structure
Date of Patent: February 5, 2002
Abstract: This invention relates to methods and apparatus for determining the multi-dimensional topology of a substance (system) within a volume (space). A method according to a preferred embodiment of the invention comprises the steps of: acquiring a set of relative values for the density (scalar properties) of the volume, each value for a given location (point) within the volume; interpolating a set of functions to generate a continuous relative density for the volume; identifying critical points of the continuous relative density by using an eigenvector following method; and associating critical points with one another by following a gradient path of the continuous relative density between the critical points, The method is applicable to a wide range of data relating to fields such as crystallography, fluid dynamics, edge detection, and financial markets, to determine the topology of structures contained therein.
US Patent Number: 4,991,191
Patent Title: Quantitative analysis of the active table ingredient by powder x-ray diffractometry
Date of Patent: February 5, 1991
Abstract: A method for quantitatively analyzing solid mixtures of a crystalline ingredient and an excipient component in commercial pharmaceutical tablets by x-ray powder diffractometry using the intact tablet as is, without special sample preparation. The method comprises the steps of: irradiating the table with x-rays in a powder x-ray diffraction device and determining the integrated intensity of diffracted x-rays, I, at an angular range producing at least one x-ray diffraction line characteristic of said crystalline ingredient; determining the ratio of said value I to a diffracted x-ray intensity value, I.sub.o, obtained on a second compressed tablet consisting of said crystalline ingredient at said angular range; and comparing the determined ratio I/I.sub.o to a set of predetermined standard values of said ratio for known mixtures of said crystalline ingredient and said excipient component to quantitate said crystalline ingredient in said first compressed tablet.
US Patent Number: 4,592,082
Patent Title: Quantitative determination of mineral composition by powder X-ray diffraction
Date of Patent: May 27, 1986
Abstract: An external standard intensity ratio method is used for quantitatively determining mineralogic compositions of samples by x-ray diffraction. The method uses ratios of x-ray intensity peaks from a single run. Constants are previously determined for each mineral which is to be quantitatively measured. Ratios of the highest intensity peak of each mineral to be quantified in the sample and the highest intensity peak of a reference mineral contained in the sample are used to calculate sample composition.
US Patent Number: 5,353,236
Patent Title: High-resolution crystallographic modelling of a macromolecule
Date of Patent: October 4, 1994
Abstract: A method for constructing an image of a macromolecular crystal includes steps of providing an envelope which defines the region of a unit cell occupied by the macromolecule; distributing a collection of scattering bodies within the envelope; condensing the collection of scattering bodies to an arrangement that maximizes the correlation between the diffraction pattern of the crystal and a pattern of Fourier amplitudes for the collection of scattering bodies; determining the phase associated with at least one of the Fourier amplitudes of the condensed collection of scattering bodies; calculating an electron density distribution of the crystal from the phase information; and defining an image of the macromolecule in the electron density distribution.
US Patent Number: 6,192,103
Patent Title: Fitting of X-ray scattering data using evolutionary algorithms
Date of Patent: February 20, 2001
Abstract: Evolutionary algorithms are used to find a global solution to the fitting of experimental X-ray scattering data to simulated models. A recombination operator combines two or more parameter vectors from one iteration of simulated scattering data to form a new parameter vector for the next iteration, in a manner such that there is a high probability that the new parameter will better fit the experimental data than any of the parent parameters. A mutation operator perturbs the value of a parent vector, to permit new regions of the error function to be examined, and thereby avoid settling on local minima. The natural selection guarantees that the parameter vectors with the best fitness will be propagated into future iterations.
US Patent Number: 6,345,235
Patent Title: Method and apparatus for determining multi-dimensional structure
Date of Patent: February 5, 2002
Abstract: This invention relates to methods and apparatus for determining the multi-dimensional topology of a substance (system) within a volume (space). A method according to a preferred embodiment of the invention comprises the steps of: acquiring a set of relative values for the density (scalar properties) of the volume, each value for a given location (point) within the volume; interpolating a set of functions to generate a continuous relative density for the volume; identifying critical points of the continuous relative density by using an eigenvector following method; and associating critical points with one another by following a gradient path of the continuous relative density between the critical points, The method is applicable to a wide range of data relating to fields such as crystallography, fluid dynamics, edge detection, and financial markets, to determine the topology of structures contained therein.
US Patent Number: 6,356,845
Patent Title: Crystallization and structure determination of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (S. aureus MurB)
Date of Patent: March 12, 2002
Abstract: The substrate free form of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (S. aureus MurB) has been crystallized, and the three dimensional x-ray crystal structure has been solved to 2.3 .ANG. resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing inhibitors of S. aureus MurB
US Patent Number: 6,131,072
Patent Title: Lane tracking system and method
Date of Patent: October 10, 2000
Abstract: A system and method for identifying lanes in images generated from DNA sequencing and fragment analysis is described. One example method includes a computer implemented method of determining the locations of lanes of separated samples. Each lane corresponds to a sample being separated by flowing the sample through a media. The method includes the following elements. Place some samples on the media. Cause the samples to separate into the lanes. Create a digital image of the lanes. Fit some curves to the lane images. Each curve corresponds to a lane formed from a separated sample.
US Patent Number: 6,128,582
Patent Title: Molecules comprising an IMPDH-like binding pocket and encoded data storage medium capable of graphically displaying them
Date of Patent: October 3, 2000
Abstract: The present invention relates to a data storage medium encoded with the corresponding structure coordinates of molecules and molecular complexes which comprise the active site binding pockets of IMPDH. Such data storage material is capable of displaying such molecules and molecular complexes, or their structural homologues, as a graphical three-dimensional representation on a computer screen. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen and design compounds, including inhibitory compounds, that bind to IMPDH or homologues thereof. This invention also relates to molecules and molecular complexes which comprise the active site binding pockets of IMPDH or close structural homologues of the active site binding pockets. This invention also relates to compounds and pharmaceutical compositions which are inhibitors of IMPDH.
US Patent Number: 6,037,949
Patent Title: Texture mapping and other uses of scalar fields on subdivision surfaces in computer graphics and animation
Date of Patent: March 14, 2000
Abstract: Methods for defining smooth scalar fields on arbitrary polygonal meshes which can be consistently carried through the subdivision process involve computing mesh vertices after subdivision to a suitable resolution and computing scalar field values at the vertices corresponding to an arbitrary smooth surface, including the limit surface. The methods allow one to define and compute the value of scalar fields over an arbitrarily dense set of points on the limit surface. Applications of these techniques in computer graphics and computer animation include: (1) the definition of pseudo-coordinates for use in parametric shading including texture mapping; (2) the assignment of smoothly varying articulation weights over the control points of a model to more efficiently define the transformation of a highly detailed object or character under specific animation controls; and (3) the assignment of smoothly varying local parameters for specifying the local behavior of dynamic or quasi-static objects or surfaces.
US Patent Number: 6,014,449
Patent Title: Computer-implemented system for analyzing rigidity of substructures within a macromolecule
Date of Patent: January 11, 2000
Abstract: A computer-implemented system and method is provided for analyzing the rigidity of substructures within a molecule represented as atomic coordinate and bond data. The system includes a preprocessor for selectively eliminating from the data those bonds below a predetermined strength to thereby generate filtered data. The system also has a data structure for representing the filtered data as a network of vertices and constraints from which rigidity information is inferred. A topography processor is provided for extracting the rigidity information from the network and constructing an index data structure to represent the extracted rigidity information. The system also includes an analyzer coupled to the index data structure for identifying rigid and floppy substructures within the molecule based on the indices.
US Patent Number: 5,752,019
Patent Title: System and method for confirmationally-flexible molecular identification
Date of Patent: May 12, 1998
Abstract: A reference storage process populates a data structure so that the data structure contains all of the molecular structures and/or rigid substructures in the database classified according to attributes of tuples. In a preferred embodiment, the tuples are derived from sites (e.g. atomic sites) of the molecular structures and the attributes can be derived from geometric (and other) information related to the tuples. The attributes are used to define indices in the data structure that are associated with invariant vector information (e.g. information about rotatable bond(s) in skewed local coordinate frames created from tuples). These representations are invariant with respect to the rotation and translation of molecular structures and/or the rotation of substructures about attached rotatable bond(s). Accordingly, the invariant vector information is classified in the data structure with the respective tuple attributes in locations determined by the index derived from the respective tuple. A matching process creates one or more tuples, skewed local reference frames, and indices (called test frame tuple indices) for the structure (substructures) of a test molecule using the same technique that was used to populate the data structure. The test frame tuple index accesses the invariant vector information and tallies the frequency of matching in order to determine the identity of molecules/substructures in the database that are structurally similar to the test molecule. This identification can be achieved even in the presence of conformationally flexible molecules in the database.
US Patent Number: 5,577,239
Patent Title: Chemical structure storage, searching and retrieval system
Date of Patent: November 19, 1996
Abstract: The present invention is a chemical structure search system and method which expands the capabilities of existing systems by capitalizing on the strengths of relational database technology. The system allows the user to optimally store and search chemical structure information including information relating to multi-valued atoms, multi-typed bonds, Markush searching and various other options in a relational database management system. The system provides a complete chemical information system which includes capabilities for: (1) exact structure searching; (2) substructure searching; (3) key searching; (4) chemical name searching; (5) molecular formula searching; (6) registration of new molecules; (7) structure import/export; and (8) data editing. Additionally, the present invention allows the routine integration of chemical structure data with other related information such as inventory, spectroscopic data and clinical data via standard relational database methods. The system also has dynamic querying capabilities which allow the user to be notified of any new chemicals that are entered into the database that are responsive to previously run queries. Furthermore, structure classes can also be implemented which allow the user to store certain types of information about particular types of chemical structures such as steroids. Accordingly, users can later call up this information in a quick and efficient manner without re-entering or performing previously run queries.
US Patent Number: 5,463,564
Patent Title: System and method of automatically generating chemical compounds with desired properties
Date of Patent: October 31, 1995
Abstract: A computer based, iterative process for generating chemical entities with defined physical, chemical and/or bioactive properties. During each iteration of the process, (1) a directed diversity chemical library is robotically generated in accordance with robotic synthesis instructions; (2) the compounds in the directed diversity chemical library are analyzed to identify compounds with the desired properties; (3) structure-property data are used to select compounds to be synthesized in the next iteration; and (4) new robotic synthesis instructions are automatically generated to control the synthesis of the directed diversity chemical library for the next iteration.
US Patent Number: 5,331,573
Patent Title: Method of design of compounds that mimic conformational features of selected peptides
Date of Patent: July 19, 1994
Abstract: A method of rational drug design includes simulating polypeptides in a way that predicts the most probable secondary and/or tertiary structures of a polypeptide, e.g., an oligopeptide, without any presumptions as to the conformation of the underlying primary or secondary structure. The method involves computer simulation of the polypeptide, and more particularly simulating a real-size primary structure in an aqueous environment, shrinking the size of the polypeptide isobarically and isothermally, and expanding the simulated polypeptide to its real size in selected time periods. A useful set of tools, termed Balaji plots, energy conformational maps, and probability maps, assist in identifying those portions of the predicted peptide structure that are most flexible or most rigid. The rational design of novel compounds, useful as drugs, e.g., bioactive peptidomimetic compounds, and constrained analogs thereof, is thus made possible using the simulation methods and tools of the described invention.
US Patent Number: 5,081,584
Patent Title: Computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide
Date of Patent: January 14, 1992
Abstract: A computer-implemented method for designing at least one anti-peptide sequence having affinity for target peptide or a fragment thereof suitable for synthesizing peptides and micromolecules, assaying for a target peptides, purifying target peptides, and/or preventing proteolyis of a polypeptide includes identification of the members of the amino acid sequence of the target peptide and their anti-sense or hydropathically complementary amino acids and determining the moving average hydropathy for the target and anti-sense members. The resulting lowest hydropathy identifies the anti-sense amino acid sequence for the target peptide. The members of the target peptide amino acid sequence are obtained along with their member-specific hydropathic values with the hydropathic values summed as a moving average. Anti-sense or complementary amino acid members are identified from the moving average information to generate an array of anti-sense amino acid sequences. The hydropathic values of the array of anti-sense amino acids are obtained along with their moving average hydropathic values from which a hydropathic complementary score is obtained with the lowest score identifying the anti-sense amino acid sequence having affinity for the target peptide.
US Patent Number: 4,939,666
Patent Title: Incremental macromolecule construction methods
Date of Patent: July 3, 1990
Abstract: A preferred embodiment of the invention is a method for constructing a polypeptide chain having a substantially predetermined conformation. Preferably a known stable well-mapped polypeptide structure is used as a starting point, and additional peptide units are incrementally added on while maintaining favorable enthalpic and entropic contributions to stability. Preferably a library of oligopeptide blocks is used to provide candidates for the additional peptide units. Preferably the library includes numerous precomputed parameters for each of the blocks, e.g. parameters for estimating energetic effects of varying the conformation parameters.
US Patent Number: 4,908,773
Patent Title: Computer designed stabilized proteins and method for producing same
Date of Patent: March 13, 19
Abstract: Proteins, such as enzymes having enhanced stability are designed through the use of a computer method. The method identifies amino acid residues of a protein which may be replaced with a cysteine residue in order to promote the formation of a protein-stabilizing disulfide bond. The computer-designed, stabilized proteins can be produced using recombinant DNA technology.
US Patent Number: 5,418,944
Patent Title: Knowledge-based molecular retrieval system and method using a hierarchy of molecular structures in the knowledge base
Date of Patent: May 23, 1995
Abstract: A molecular retrieval system and method answering to similarity queries for retrieving molecular structures, stored into a source database (22) and having a required similarity with an input structure, which can contain a set of property regions. A target database (23) stores the molecular structures described in hierarchical way and a knowledge base (24) stores well-known molecular fragments at different levels of description together with a set of physical and chemical properties associated to each fragment. A fragment recognizer (21) analyzes the fragments of the input structure to represent them in a hierarchical way. A query analyzer (25) analyzes the similarity queries and selects the appropriate level of molecular representation on the basis of the required similarity. Matching means (26, 27, 29), when called by the query analyzer (25), perform a matching of the representation of the input structure against the representations of the molecular structures stored into the target database (23) at the selected level of molecular representation.
US Patent Number: 5,386,507
Patent Title: Computer graphics system for selectively modelling molecules and investigating the chemical and physical properties thereof
Date of Patent: January 31, 1995
Abstract: A computer graphics system for modeling chemical molecules includes simultaneous two-dimensional and three-dimensional display of models of molecules from a single data set, and allows a user to edit in either two dimensions or three dimensions. A two-dimensional model may be stylized while a three-dimensional model of the same molecule remains chemically (geometrically) correct. The system has editing tools for use in both two dimensions and three dimensions, and changes made in one mode are immediately reflected in the other, and the editing tools include manipulation components for the user to display on elements of a model, and to use to move parts of a model of a molecule relative to other parts. The system includes techniques for structure determination and display that significantly reduce the computer power required to perform system functions, rendering techniques formally reserved to supercomputers usable on smaller computer platforms. Physically based modeling is included, allowing the user to perturb the geometry of a model and to investigate interactively the effects of perturbation according to a dynamic force equation. The system also includes a procedure for displaying multiple models of molecules and performing docking studies between the models.
US Patent Number: 4,980,840
Patent Title: Computerized editing and composing system
Date of Patent: December 25, 1990
Abstract: A computerized editing and composing system and method which conveniently and directly edits and composes complex scientific formulas, chemical structural formulas and music staves. The system comprises a computer, an I/O interface, an input device, a character library and character generating system, a display, an editing and composing process device and peripheral devices, and automatically processes the corresponding text while providing the user with a simple and convenient operational interface with inputting, editing, composing and outputting techniques to generate the different resolutions of the output.
US Patent Number: 4,855,931
Patent Title: Stochastic method for finding molecular conformations
Date of Patent: August 8, 1989
Abstract: This is a stochastic method for determining the likely conformations of a molecule by starting with an initial molecular structure along with given atomic coordinate positions and defined bonds between atoms. Each of the atom's initial X, Y and Z coordinates are modified by the combination therewith of random numbers to create a new random coordinate position for each atom. A predetermined constraint is placed on the distance of each new coordinate from each initial coordinate. The steric energy of the reconfigured molecule is then calculated, stored and a new set of randon numbers combined with the atomic coordinates and the steric energy of the new structure calculated. The process is repeated until most, if not all, steric minima are detected and the structures associated therewith are determined.
US Patent Number: 4,835,528
Patent Title: Cursor control system
Date of Patent: May 30, 1989
Abstract: A cursor control system for computer displays moves a cursor unambiguously in three dimensions using a two dimensional input device. The plane of movement of the two dimensional device is divided into logical regions which correspond to movement along a three dimensional axis. Movement of the two dimensional device into one of these regions causes the cursor to move along the corresponding axis of the display.
US Patent Number: 4,473,890
Patent Title: Method and device for storing stereochemical information about chemical compounds
Date of Patent: September 25, 1984
Abstract: The structure of a compound is expressed as an atom connection table using an electronic computer. The structure is registered in a three-dimensional manner, making it possible to effect the interconversion between the atom connection table and symbols R, S that represent absolute configuration of asymmetric carbon atoms, or .alpha., .beta. that represent directions of substitution relative to the plane the ring. Namely, in the case of a ring compound, bonded atoms in the clockwise and counterclockwise directions, and bonded atoms in the upward and downward directions of the ring are stored in the separate predetermined registers. In the case of a chain compound, bonded atoms in the right and left directions, and bonded atoms in the upward and downward directions are stored in the separate predetermined registers. On the atom connection table, therefore, the rotational directing of bonded atoms can be defined as viewed from a given direction. It is therefore possible to prepare the atom connection table reflecting the symbols in the compound name, to store three-dimensional structures of compounds, and to process and produce the data.
US Patent Number: 5,379,234
Patent Title: Computer-aided chemical illustration system
Date of Patent: January 3, 1995
Abstract: A computer-aided chemical illustration system is disclosed. Techniques provided include: 1) efficient drawing of bonds; 2) drawing different bond types during a single mode; 3) determining bisect angles for bonds; 4) labeling atoms on the fly; 5) automatic alignment of atom labels; 6) custom alignment of atom labels; 7) changing the type, style, or orientation of an object while it is being drawn; 8) detection of ring structures; and 9) shifting bonds around on a ring.
US Patent Number: 5,056,035
Patent Title: Method for processing information on chemical reactions
Date of Patent: October 8, 1991
Abstract: A method for processing information of chemical reactions of producing at least one product from at least one starting material, said information being given in the form of imaginary transition structures (ITS) in which the starting material is topologically superposed upon the product and bonds are distinguished and classified into three categories of (1) bonds linking two nodes appearing both in the starting and product stages, (2) bonds linking two nodes appearing only in the starting stage and (3) bonds linking two nodes appearing only in the product stage and/or in the form of connection tables of ITS, which comprises extracting from the imaginary transition structure and/or the connection table a reaction string composed of said bonds (2) and said bonds (3) which are alternately arranged to each other.
US Patent Number: 5,025,388
Patent Title: Comparative molecular field analysis (CoMFA)
Date of Patent: June 18, 1991
Abstract: Comparative Molecular Field Analysis (CoMFA) is an effective computer implemented methodology of 3D-QSAR employing both interactive graphics and statistical techniques for correlating shapes of molecules with their observed biological properties. For each molecule of a series of known substrates the steric and electrostatic interaction energies with a test probe atom are calculated at spatial coordinates around the molecule. Subsequent analysis of the data table by a partial least squares (PLS) cross-validation technique yields a set of coefficients which reflect the relative contribution of the shape elements of the molecular series to differences in biological activities. Display in three dimensions in an interactive graphics environment of the spatial volumes highly associated with biological activity, and comparison with molecular structures yields an understanding of intermolecular associations. CoMFA will also predict the biological activity of new molecular species.
US Patent Number: 5,555,366
Patent Title: Computer graphics system for selectively modelling molecules and investigating the chemical and physical properties thereof
Date of Patent: September 10, 1996
Abstract: A computer graphics system for modeling chemical molecules includes simultaneous two-dimensional and three-dimensional display of models of molecules from a single data set, and allows a user to edit in either two dimensions or three dimensions. A two-dimensional model may be stylized while a three-dimensional model of the same molecule remains chemically (geometrically) correct. The system has editing tools for use in both two dimensions and three dimensions, and changes made in one mode are immediately reflected in the other, and the editing tools include manipulation components for the user to display on elements of a model, and to use to move parts of a model of a molecule relative to other parts. The system includes techniques for structure determination and display that significantly reduce the computer power required to perform system functions, rendering techniques formally reserved to supercomputers usable on smaller computer platforms. Physically based modeling is included, allowing the user to perturb the geometry of a model and to investigate interactively the effects of perturbation according to a dynamic force equation. The system also includes a procedure for displaying multiple models of molecules and performing docking studies between the models.
US Patent Number: 5,424,963
Patent Title: Molecular dynamics simulation method and apparatus
Date of Patent: June 13, 1995
Abstract: A computer-assisted method for generating a dynamic model of a molecule is described based on information of the atomic structure. The model data is defined by rigid bodies corresponding to groups of atoms of the molecule with substantially no relative movement between the atoms, flexible bodies corresponding to groups of atoms which are characterized by relative movement between the atoms, and flexure elements which define an interconnection of two of the rigid bodies and the flexible bodies and predetermined degrees of freedom.
US Patent Number: 4,811,217
Patent Title: Method of storing and searching chemical structure data
Date of Patent: March 7, 1989
Abstract: Chemical structure data containing generic representation of component atoms in a storage device is searched by finding a match between a query structure and a stored candidate structure by mathematically comparing attribute data of chemical units of a query structure and attribute data of chemical unit of a stored candidate structure, where attribute data represent chemical characteristics of chemical units of those structures.
US Patent Number: 5,619,421
Patent Title: Computer-implemented process and computer system for estimating the three-dimensional shape of a ring-shaped molecule and of a portion of a molecule containing a ring-shaped structure
Date of Patent: April 8, 1997
Abstract: A computer-implemented process determines candidate three-dimensional shapes of ring-shaped molecules through an exhaustive search of combinations of torsion angles of the bonds of the ring, given known bond lengths and bond angles for the bonds between atoms of the rings, a range of torsion angles and a resolution. Candidate combinations of the torsion angles are selected according to the range and resolution and coordinates of the atoms of the ring are determined for each candidate combination. It is then determined whether each candidate combination defines a physically possible ring. Indications of such candidate combinations are recorded. Candidate combination may then be selected from those recorded so that coordinates of atoms in candidate repetitive structures may be determined.
US Patent Number: 5,930,784
Patent Title: Method of locating related items in a geometric space for data mining
Date of Patent: July 27, 1999
Abstract: A method for locating related items in a geometric space transforms relationships among items to geometric locations. The method locates items in the geometric space so that the distance between items corresponds to the degree of relatedness. The method facilitates communication of the structure of the relationships among the items. The method is especially beneficial for communicating databases with many items, and with non-regular relationship patterns. Examples of such databases include databases containing items such as scientific papers or patents, related by citations or keywords. A computer system adapted for practice of the present invention can include a processor, a storage subsystem, a display device, and computer software to direct the location and display of the entities. The method comprises assigning numeric values as a measure of similarity between each pairing of items. A matrix is constructed, based on the numeric values. The eigenvectors and eigenvalues of the matrix are determined. Each item is located in the geometric space at coordinates determined from the eigenvectors and eigenvalues. Proper construction of the matrix and proper determination of coordinates from eigenvectors can ensure that distance between items in the geometric space is representative of the numeric value measure of the items' similarity.
US Patent Number: 5,884,230
Patent Title: Method and system for protein modeling
Date of Patent: March 16, 1999
Abstract: A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In one embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of the backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. In another embodiment, the modeling of a variable region of the model protein is based on a collection of .psi. and .phi. angle values for amino acid pairs in a family of proteins. In a further embodiment, these .psi. and .phi. angle values are classified according to a tetramer of adjacent amino acids and filtered based on a most probable conformation of portions of the variable region of the model protein.
US Patent Number: 5,557,535
Patent Title: Method and system for protein modeling
Date of Patent: September 17, 1996
Abstract: A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In a preferred embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. The proteins comprise a plurality of amino acids having backbone atoms and side chain atoms. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of each backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. The inter-atomic distance constraints for each pair of atoms with an established position is generated. Finally, the position of each atom in the model protein is set so that the inter-atomic distances are in accordance with the constraints.
US Patent Number: 5,764,872
Patent Title: Method and system for displaying vector data as stream lines in a space represented by tetrahedral cells
Date of Patent: June 9, 1998
Abstract: A method and apparatus for displaying stream lines in a space are disclosed. First, the space is divided into a plurality of tetrahedral cells. Position data of each vertex of the tetrahedral cells and vector data at each position are collected. A critical point for each tetrahedral cell is then computed. The critical point is within the tetrahedral cell and for which the vector data becomes zero. Using the collected position and vector data, a Jacobian matrix J is calculated when such a critical point is found, and eigenvalues of the Jacobian matrix J are also calculated. Next, the starting point of a stream line within a tetrahedral cell is calculated for each of the eigenvalues by moving a microscopic distance from the critical point. Finally, a stream line is calculated from the starting point, and the stream line is displayed.
US Patent Number: 6,438,204
Patent Title: Linear prediction of structure factors in x-ray crystallography
Date of Patent: August 20, 2002
Abstract: A method uses linear prediction analysis to define a first structure factor component for a first reflection from x-ray crystallography data. The x-ray crystallography data includes a set of cognizable reflections. The method includes expressing the first structure factor component as a first linear equation in which the first structure factor component is equal to a sum of a first plurality of terms. Each term includes a product of (1) a structure factor component for a cognizable reflection from the x-ray crystallography data, wherein the cognizable reflection has a separation in reciprocal space from the first reflection, and (2) a linear prediction coefficient corresponding to the separation between the cognizable reflection and the first reflection. The method further includes calculating values for the linear prediction coefficients. The method further includes substituting the values for the linear prediction coefficients into the first linear equation, thereby defining the first structure factor component for the first reflection.
US Patent Number: 5,200,910
Patent Title: Method for modelling the electron density of a crystal
Date of Patent: April 6, 1993
Abstract: A method for modelling the electron density distribution of a macromolecule in a defined asymmetric unit of a crystal lattice having locations of uniformly diffracting electron density includes the steps of: producing an initial distribution of scattering bodies within a asymmetric unit having the same dimensions as the defined asymmetric unit; calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the normalized amplitudes; moving at least one of the scattering bodies within the asymmetric unit to create a modified distribution; calculating scattering amplitudes and phases of the modified distribution and determining the correlation between the calculated amplitudes and the normalized values; and producing a final distribution of scattering bodies by repeating moving and calculating steps until the correlation between the calculated scattering amplitudes and the normalized amplitudes is effectively maximized, the final distribution of scattering bodies defining the electron density of the crystal.
US Patent Number: 5,241,470
Patent Title: Prediction of protein side-chain conformation by packing optimization
Date of Patent: August 31, 1993
Abstract: A method is provided for determining the packing conformation of amino acid side chains on a fixed peptide backbone. Using a steric interaction potential, the side chain atoms are rotated about carbon-carbon bonds such that the side chains preferably settle in a low energy packing conformation. Rotational moves are continued according to a simulated annealing procedure until a set of low energy conformations are identified. These conformations represent the structure of the actual peptide. The method may be employed to identify the packing configuration of mutant peptides.
US Patent Number: 5,365,456
Patent Title: Method for modelling the electron density of a crystal
Date of Patent: November 15, 1994
Abstract: A method for modelling the electron density distribution of a macromolecule in a defined asymmetric unit of a crystal lattice having locations of uniformly diffracting electron density includes the steps of: producing an initial distribution of scattering bodies with a asymmetric unit having the same dimensions as the defined asymmetric unit; calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the normalized amplitudes; moving at least one of the scattering bodies within the asymmetric unit to create a modified distribution; calculating scattering amplitudes and phases of the modified distribution and determining the correlation between the calculated amplitudes and producing a final distribution of scattering bodies by repeating moving and calculating steps until the correlation between the calculated scattering amplitudes and the normalized amplitudes is effectively maximized, the final distribution of scattering bodies defining the electron density of the crystal.
US Patent Number: 6,408,047
Patent Title: Method of providing high throughput protein crystallography
Date of Patent: June 18, 2002
Abstract: The invention provides a method of performing x-ray crystallography on samples by using a robot to select the target sample, to position the sample for x-ray crystallography, and to deposit the sample, all without transferring the sample to another device, such as a goniometer. This method allows high throughput, automated crystallography, thereby providing a high volume of samples to be tested while lessening the need for human intervention.
US Patent Number: 6,404,849
Patent Title: Automated sample handling for X-ray crystallography
Date of Patent: June 11, 2002
Abstract: Method and apparatus for mounting a sample comprising a crystal for X-ray crystallographic analysis, a method for aligning a sample comprising a crystal for X-ray crystallographic analysis, which sample is mounted on a positioning device, and a method for determining the structure of a sample containing a crystal by means of X-ray crystallography.
US Patent Number: 6,400,797
Patent Title: Sample changer for capillary geometry X-ray diffractometers
Date of Patent: June 4, 2002
Abstract: This present invention provides a sample changer for automatically changing from one sample to the next in support of high throughput X-ray powder diffraction data acquisition in a capillary geometry. The samples are mounted on the outer rim of a disk or turntable, with each sample having its capillary axis parallel to a radius emanating from the center of the disk on which the samples are mounted. Each sample is mounted on a separate motor shaft which permits the sample to be rotated about the longitudinal axis of the capillary during data acquisition. To change from one sample to the next, the disk or turntable is rotated about its axis thereby presenting in turn each new sample to a X-ray beam. When the data acquisition is completed for that sample, a new sample is rotated into the beam and its data collection is carried out.
US Patent Number: 6,111,930
Patent Title: Automatic sample changer for an X-ray diffractometer
Date of Patent: August 29, 2000
Abstract: A sample changer (2) for the automatic intake of a multitude of samples into the measurement position on the goniometer axis (a) of an X-ray diffractometer (20) in which the individual samples--each showing a surface, which meets the goniometer axis at a tangent in the measurement position--are linearly arranged on an insertable magazine (3). The samples on the magazine (3) can be moved in the direction of the goniometer axis (a) in order to transport each sample translationally into the measurement position. Furthermore the sample changer (2), the magazine (3) and the mountings (10) show recesses, which allow the refracted X-ray beams from the sample in transmission mode to pass through to the detector (14) unimpeded. The sample changer is suitable for reflection mode as well as transmission mode measurements without having to redesign the system.
US Patent Number: 5,127,039
Patent Title: Sample holder for X-ray diffractometry
Date of Patent: June 30, 1992
Abstract: A sample holder for use with X-ray diffractometers with the capability to rotate the sample, as well as to adjust the position of the sample in the x, y, and z directions. Adjustment in the x direction is accomplished through loosening set screws, moving a platform, and retightening the set screws. Motion translators are used for adjustment in the y and z directions. An electric motor rotates the sample, and receives power from the diffractometer.
US Patent Number: 4,770,593
Patent Title: Sample changer for X-ray diffractometer
Date of Patent: September 13, 1988
Abstract: A sample changer for powder X-ray diffractometry includes a cylindrical dispensing container for holding a stack of pre-test sample holders, a cylindrical receiving container for holding a stack of post-test sample holders and a changer arm which automatically picks up the topmost sample disk in the dispensing container and rotatably positions the sample disk on the sample holder stage of an X-ray diffractometer for analysis. After analysis, the changer arm removes the sample holder and releases it into the receving container. The sample holders have a circumferential groove which coacts with semi-circular rotatable cams positioned on the distal end of the changer arm to enable the changer arm to lift and place the sample holders.
US Patent Number: 4,641,329
Patent Title: Fixture for supporting and aligning a sample to be analyzed in an X-ray diffraction apparatus
Date of Patent: February 3, 1987
Abstract: A fixture is provided for supporting and aligning small samples of material on a goniometer for X-ray diffraction analysis. A sample-containing capillary is accurately positioned for rotation in the X-ray beam by selectively adjusting the fixture to position the capillary relative to the x and y axes thereof to prevent wobble and position the sample along the z axis or the axis of rotation. By employing the subject fixture relatively small samples of materials can be analyzed in an X-ray diffraction apparatus previously limited to the analysis of much larger samples.
US Patent Number: 6,371,640
Patent Title: Apparatus and method for characterizing libraries of different materials using X-ray scattering
Date of Patent: April 16, 2002
Abstract: An apparatus for characterizing a library is provided in which the library contains an array of elements and each element contains a different combination of materials. The apparatus includes an x-ray beam directed at the library, a chamber which houses the library and a beamline for directing the x-ray beam onto the library in the chamber. The chamber may include a translation stage that holds the library and that is programmable to change the position of the library relative to the x-ray beam and a controller that controls the movement of the translation stage to expose an element to the x-ray beam in order to rapidly characterize the element in the library. During the characterization, the x-ray beam scatters off of the element and a detector detects the scattered x-ray beam in order to generate characterization data for the element.
US Patent Number: 5,600,571
Patent Title: Method for determining protein tertiary structure
Date of Patent: February 4, 1997
Abstract: The subject invention provides a method for determining the most stable tertiary structure of a protein having a known primary structure which comprises the steps of (a) producing a reduced representation of the protein by assigning to the protein (i) all secondary structural motifs present therein and (ii) all .phi. and .PHI. dihedral angles for the amino acid residues present therein; (b) determining which conformations of the reduced representation are physically permissible, so as to determine which conformations of the protein are physically permissible; and (c) determining which of the physically permissible conformations of the protein possesses the lowest free energy, so as to thereby determine the most stable tertiary structure of the protein.
US Patent Number: 5,265,030
Patent Title: System and method for determining three-dimensional structures of proteins
Date of Patent: November 23, 1993
Abstract: A computer system and method are disclosed for determining a protein's tertiary structure from a primary sequence of amino acid residues. The system uses a dynamic Monte Carlo method with Metropolis sampling criterion, and a selected (2,1,0) lattice model, to simulate protein folding during the transition of the protein from an unfolded (denatured) state to its native, folded state. The system generates, for display, a folding trajectory representing successive three-dimensional images of the protein at a level of two Angstrom resolution as it folds to its native conformation. The system permits interaction between all proximate pairs of sidechains of the protein and provides faster processing through the use of the lattice. The system comprises an input means such as a keyboard for specifying (entering) selected amino acid sequences and other data such as temperature and fold preferences, a RAM (random access memory) for storing such data, a ROM (read-only memory) with a stored program, a CRT (cathode ray tube) display unit and/or printer, an optional auxiliary disc storage device for storage of relevant data bases, and a microprocessor for processing the entered data, for simulating, under control of the stored program, the folding of the protein from its unfolded state to its folded (tertiary) state, and for displaying via the display unit (or printer) tertiary conformations of the protein in three dimensions.
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