| 序号 | 专利名 | 申请号 | 申请日 | 公开（公告）号 | 公开（公告）日 | 发明人 |
|---|---|---|---|---|---|---|
| 81 | ESTIMATION OF PROTEIN-COMPOUND INTERACTION AND RATIONAL DESIGN OF COMPOUND LIBRARY BASED ON CHEMICAL GENOMIC INFORMATION | US12274744 | 2008-11-20 | US20100099891A1 | 2010-04-22 | Yasushi OKUNO; Kei TANEISHI; Gozoh TSUJIMOTO |
| A data processing method for an estimation of compound-protein interaction using both chemical substance information, such as a chemical property of the compound, and biological information, such as sequence information of genes to rationally and efficiently screen compounds. First space representing space coordinates of a first chemical substance group and second space representing space coordinates of a second chemical substance group are defined, and the first chemical substance group is characterized by a first characteristic amount and the second chemical substance group is characterized by a second characteristic amount, and map transformation of the coordinates of the first space and the coordinates of the second space results in the solution so as to increase the correlation between the first space and the second space using a multivariable analysis technique or a machine learning method. | ||||||
| 82 | METHODS FOR IDENTIFYING SETS OF OLIGONUCLEOTIDES FOR USE IN AN IN VITRO RECOMBINATION PROCEDURE | US12557463 | 2009-09-10 | US20100056385A1 | 2010-03-04 | Sergey A. Selifonov; Willem P.C. Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip A. Patten; Jeremy Minshull; Lorraine J. Giver |
| In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. | ||||||
| 83 | Computer based method for identifying peptides useful as drug targets | US09539032 | 2000-03-30 | US07657378B1 | 2010-02-02 | Samir Kumar Brahmachari; Debasis Dash |
| The present invention relates to a novel computer based method for performing genome-wise comparison of several organisms, the said computational method involves creation of peptide libraries from protein sequences of several organisms and subsequent comparison leading to identification of conserved invariant peptide motifs, and to this end several invariant peptide motifs have been identified by direct sequence comparison between various bacterial organisms and host genomes without any a priori assumptions, and the present method is useful for identification of potential drug targets and can serve as drug screen for broad-spectrum antibacterials as well as for specific diagnosis of infections, and in addition, for assignment of function to proteins of yet unknown functions with the help of such invariant peptide motif signatures. | ||||||
| 84 | Methods for identifying sets of oligonucleotides for use in an in vitro recombination procedure | US11339090 | 2006-01-24 | US07620502B2 | 2009-11-17 | Sergey A. Selifonov; Willem P. C. Stemmer; Claes Gustafsson; Matthew Tobin; Stephen del Cardayre; Phillip A. Patten; Jeremy Minshull; Lorraine J. Giver |
| In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators are used to identify sets of oligonucleotides for in vitro recombination. | ||||||
| 85 | Optimization of crossover points for directed evolution | US10386903 | 2003-03-10 | US07620500B2 | 2009-11-17 | Emily C. Mundorff; Sridhar Govindarajan; Claes Gustafsson; Jeremy S. Minshull |
| Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination. | ||||||
| 86 | Methods, systems, and software for identifying functional biomolecules | US11981577 | 2007-10-30 | US20080133143A1 | 2008-06-05 | Claes Gustafsson; Sridhar Govindarajan; Robin A. Emig; Richard John Fox; Ajoy K. Roy; Jeremy S. Minshull; S. Christopher Davis; Anthony R. Cox; Phillip A. Patten; Linda A. Castle; Daniel L. Siehl; Rebecca Lynne Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 87 | Methods, systems, and software for identifying functional biomolecules | US11981578 | 2007-10-30 | US20080132416A1 | 2008-06-05 | Richard John Fox |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 88 | System of components for preparing oligonucleotides | US09067638 | 1998-04-28 | US07321828B2 | 2008-01-22 | Lex M. Cowsert; Brenda F. Baker; John McNeil; Susan M. Freier; Henri M. Sasmor; Douglas G. Brooks; Cara Ohashi; Jacqueline R. Wyatt; Alexander H. Borchers; Timothy A. Vickers |
| Interative, preferably computer based iterative processes for generating synthetic compounds with desired physical, chemical and/or bioactive properties, i.e., active compounds, are provided. During iterations of the processes, a target nucleic acid sequence is provided or selected, and a library of candidate nucleobase sequences is generated in silico according to defined criteria. A “virtual” oligonucleotide chemistry is chosen and a library of virtual oligonucleotide compounds having the selected nucleobase sequences is generated. These virtual compounds are reviewed and compounds predicted to have particular properties are selected. The selected compounds are robotically synthesized and are preferably robotically assayed for a desired physical, chemical or biological activity. Active compounds are thus generated and, at the same time, preferred sequences and regions of the target nucleic acid that are amenable to oligonucleotide or sequence-based modulation are identified. | ||||||
| 89 | Computer-implemented method of merging libraries of molecules using validated molecular structural descriptors and neighborhood distances to maximize diversity and minimize redundancy | US09776711 | 2001-02-05 | US07096162B2 | 2006-08-22 | Richard D. Cramer; David E. Patterson |
| The use for biological screening purposes of a subset (library) of a large combinatorially accessible chemical universe increases the efficiency of the screening process only if the subset contains members representative of the total diversity of the universe. In order to insure inclusion in the subset of molecules representing the total diversity of the universe under consideration, valid molecular descriptors which quantitatively reflect the diversity of the molecules in the universe are required. A unique validation method is used to examine both a new three dimensional steric metric and some prior art metrics. With this method, the relative usefulness/validity of individual metrics can be ascertained from their application to randomly selected literature data sets. By the appropriate application of validated metrics, the method of this invention selects a subset of a combinatorial accessible chemical universe such that the molecules of the subset are representative of all the diversity present in the universe and yet do not contain multiple members which represent the same diversity (oversample). The use of the neighborhood definition of a validated metric may also be used to combine (without oversampling the same diversity) any number of combinatorial screening libraries. | ||||||
| 90 | Methods and apparatus for preparing high-dimensional combinatorial experiments | US10024649 | 2001-12-17 | US06996550B2 | 2006-02-07 | Youqi Wang; Marco Falcioni; Stephen J. Turner; C. Eric Ramberg |
| Computer-implemented methods, systems and apparatus, including computer program apparatus, provide techniques for designing a set of experiments to be performed with a set of resources. A plurality of experimental configurations are generated based on a set of parameters describing factors to be varied in the experiments and a set of constraints representing limitations on operations that can be performed with the set of resources. A set of experiments is defined based on a selected configuration. The constraints can be represented as patterns defining an application of a parameter to a set of one or more points of an experimental lattice. | ||||||
| 91 | Cell based binning methods and cell coverage system for molecule selection | US09564210 | 2000-05-04 | US06850876B1 | 2005-02-01 | Raymond L. H. Lam; William J. Welch; Sidney Stanley Young |
| A cell-based binning method (“Data Driven” binning method) allows the inclusion of all molecules, generates a high percentage of occupied cells, and provides adequate division of the molecules in the low-dimensional subspaces (typically all one-dimension (1-D), two-dimension (2-D), and three-dimension (3-D) subspaces). A chemical space coverage criterion (“Uniform Cell Coverage (UCC)” criterion) measures the uniformity of coverage of the molecules selected. A fast exchange design algorithm (“fast exchange UCC” algorithm) that minimizes the number of searches of the candidate points while maximizing the number of exchanges during each pass through the candidate points. This method is many times faster than previous exchange algorithms and generates designs with good coverage properties. | ||||||
| 92 | Methods, systems, and software for identifying functional biomolecules | US10629351 | 2003-07-29 | US20040161796A1 | 2004-08-19 | Claes Gustafsson; Sridhar Govindarajan; Robin A. Emig; Richard John Fox; Ajoy K. Roy; Jeremy S. Minshull; S. Christopher Davis; Anthony R. Cox; Phillip A. Patten; Linda A. Castle; Daniel L. Siehl; Rebecca Lynne Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 93 | Method of identifying candidate molecules | US09693731 | 2000-10-20 | US06727100B1 | 2004-04-27 | Daniel Vitt; Stefan Busemann; Ulrich Dauer |
| A method of identifying candidate molecules expected to be biologically active comprises the following steps: Creating a set consisting of different molecules; to each of said molecules of said set, assigning a descriptor representing a predetermined number of molecular properties; mapping said set of molecules onto points of a two-dimensional grid with regard to a predetermined similarity relation of the respective assigned descriptors such that the grid distance between grid points of two molecules is a measure for the similarity of said two molecule descriptors; forming a three-dimensional surface over said grid of molecules, said surface representing the distribution of biological activity of the molecules on the grid approximatively according to a predetermined quality criterion; selecting from said three-dimensional surface candidate molecules satisfying a predetermined criterion with respect to their biological activity. | ||||||
| 94 | Methods, systems, and software for identifying functional biomolecules | US10379378 | 2003-03-03 | US20040072245A1 | 2004-04-15 | Claes Gustafsson; Sridhar Govindarajan; Robin A. Emig; Richard John Fox; Ajoy K. Roy; Jeremy S. Minshull; S. Christopher Davis; Anthony R. Cox; Phillip A. Patten; Linda A. Castle; Daniel L. Siehl; Rebecca Lynne Gorton; Teddy Chen |
| The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | ||||||
| 95 | Apparatus and method for designing proteins and protein libraries | US09877695 | 2001-06-08 | US20020147547A1 | 2002-10-10 | John R. Desjarlais |
| Methodology for the automated design of proteins is disclosed. Various methods executed by a computer for generating probability matrices, protein sequences, combinatorial libraries of proteins, and optimization of various parameters related to protein design are disclosed. Methodology is applicable to the design and analysis of protein structures and protein sequences. | ||||||
| 96 | Method, system, and computer program product for analyzing combinatorial libraries | US10058216 | 2002-01-29 | US20020143476A1 | 2002-10-03 | Dimitris K. Agrafiotis; Victor S. Lobanov; Francis R. Salemme |
| The invention provides for in silico analysis of a virtual combinatorial library. Mapping coordinates for a training subset of products in the combinatorial library, and features of their building blocks, are obtained. A supervised machine learning approach is used to infer a mapping function null that transforms the building block features for each product in the training subset of products to the corresponding mapping coordinates for each product in the training subset of products. The mapping function null is then encoded in a computer readable medium. The mapping function null can be retrieved and used to generate mapping coordinates for any product in the combinatorial library from the building block features associated with the product. | ||||||
| 97 | Method for planning the generation of combinatorial chemistry libraries method for planning the generation of combinatorial chemistry libraries | US09488771 | 2000-01-21 | US06377895B1 | 2002-04-23 | Eric G. Horlbeck |
| A computer-implemented method and apparatus are provided for planning the generation of combinatorial chemical libraries produced by a series of chemical reaction stages, each stage involving a multiplicity of simultaneous chemical reactions utilizing a set of potential synthons. The disclosed method and apparatus involve enumerating the members of the proposed library and determining which of the members meet desired criteria. | ||||||
| 98 | Generation of virtual combinatorial libraries of compounds | US09076405 | 1998-05-12 | US06253168B1 | 2001-06-26 | Richard Griffey; Eric Swayze |
| The present invention provides methods for the generation of virtual libraries of compounds. These compounds are generated in silico. The present invention encompasses methods for tracking the addition of fragments, use of reagents, and transformations performed. Further, methods for interfacing the information necessary to generate libraries of compounds with instrumentation that conducts the actual synthesis of the compounds are provided. Also provided are methods for the in silico docking of the library compounds to identified target molecules of interest. | ||||||
| 99 | Further method of creating and rapidly searching a virtual library of potential molecules using validated molecular structural descriptors | US08903217 | 1997-07-20 | US06240374B1 | 2001-05-29 | Richard D. Cramer; David E. Patterson |
| The problem of how to select out of a large chemically accessible universe molecules representative of the diversity of that universe is resolved by the discovery of a method to validate molecular structural descriptors. Using the validated descriptors, optimally diverse subsets can be selected. In addition, from the universe, molecules with characteristics similar to a selected molecule can be identified. The validated descriptors also enable the generation of a huge virtual library of potential product molecules which could be formed by combinatorial arrangement of structural variations and cores. In this virtual library it is possible to search billions of possible product compounds in relatively short time frames. | ||||||
| 100 | System, method, and computer program for at least partially automatically generating chemical compounds having desired properties | US698246 | 1996-08-15 | US5684711A | 1997-11-04 | Dimitris K. Agrafiotis; Roger F. Bone; Francis R. Salemme; Richard M. Soll |
| 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. | ||||||
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