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1. 发明授权

US06892139B2 Determining the functions and interactions of proteins by comparative analysis 有权
标题翻译：通过比较分析确定蛋白质的功能和相互作用
公开(公告)号：US06892139B2
公开(公告)日：2005-05-10
申请号：US09712363
申请日：2000-11-13
申请人： David Eisenberg , Sergio H. Rotstein , Edward M. Marcotte
发明人： David Eisenberg , Sergio H. Rotstein , Edward M. Marcotte
IPC分类号： G06F19/00 , G01N33/48 , C12Q1/68 , G01N33/50
CPC分类号： G06F19/18 , G06F19/22
摘要： The invention provides novel methods for characterizing the function of nucleic acids and polypeptides. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The characterization is based on use of methods of the invention comprising algorithms that can identify functional relationships between diverse sets of non-homologous nucleic acid and polypeptide sequences. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The invention provides a computer system, comprising a processor and a computer program product of the invention.
摘要翻译：本发明提供用于表征核酸和多肽的功能的新方法。本发明提供了用于鉴定可能是药物靶标的核酸或多肽序列的新方法。本发明提供了一种用于鉴定可能对生物体的生长或活力至关重要的核酸或多肽序列的新方法。该表征基于本发明的方法的使用，其包括可以鉴定不同组非同源核酸和多肽序列之间的功能关系的算法。本发明提供了一种计算机程序产品，其存储在计算机可读介质上，用于鉴定可能对生物体的生长或活力至关重要的核酸或多肽序列。本发明提供了一种计算机程序产品，其存储在计算机可读介质上，用于鉴定可能是药物靶标的核酸或多肽序列。本发明提供一种包括本发明的处理器和计算机程序产品的计算机系统。

2. 发明授权

US06466874B1 Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences 有权
标题翻译：用于从基因组序列检测蛋白质功能和蛋白质 - 蛋白质相互作用的Rosetta石方法
公开(公告)号：US06466874B1
公开(公告)日：2002-10-15
申请号：US09493497
申请日：2000-01-28
申请人： David Eisenberg , Edward M. Marcotte , Matteo Pellegrini , Michael J. Thompson , Todd O. Yeates
发明人： David Eisenberg , Edward M. Marcotte , Matteo Pellegrini , Michael J. Thompson , Todd O. Yeates
IPC分类号： G06F1900
CPC分类号： G06F19/14 , G06F19/18 , G06F19/22
摘要： A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A′ and B′ have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A′ and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.
摘要翻译：提供了一种计算方法系统和计算机程序，用于从基因组序列推断功能链接。一种方法是基于一些观察结果，一些蛋白质A'和B'在另一个生物融合成单个蛋白质链AB的同源物。序列的跨基因组比较可以揭示这些AB序列，它们是Rosetta Stone序列，因为它们破译了A'和B之间的相互作用。另一种方法比较了两种或更多种生物体的基因组序列，以创建每种蛋白质的系统发育谱，存在或不存在所有基因组。该资料提供了不同蛋白质家族之间的功能链接信息。在另一种方法中，使用上述两种方法的组合来预测功能链接。

3. 发明授权

US06564151B1 Assigning protein functions by comparative genome analysis protein phylogenetic profiles 有权
标题翻译：通过比较基因组分析蛋白质系统发育谱来分配蛋白质功能
公开(公告)号：US06564151B1
公开(公告)日：2003-05-13
申请号：US09493498
申请日：2000-01-28
申请人： Matteo Pellegrini , Edward M. Marcotte , Michael J. Thompson , David Eisenberg , Robert Grothe , Todd O. Yeates
发明人： Matteo Pellegrini , Edward M. Marcotte , Michael J. Thompson , David Eisenberg , Robert Grothe , Todd O. Yeates
IPC分类号： G06F1900
CPC分类号： G06F19/14 , G06F19/18 , G06F19/22
摘要： A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A′ and B′ have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A′ and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.
摘要翻译：提供了一种计算方法系统和计算机程序，用于从基因组序列推断功能链接。一种方法是基于一些观察结果，一些蛋白质A'和B'在另一个生物融合成单个蛋白质链AB的同源物。序列的跨基因组比较可以揭示这些AB序列，它们是Rosetta Stone序列，因为它们破译了A'和B之间的相互作用。另一种方法比较了两种或更多种生物体的基因组序列，以创建每种蛋白质的系统发育谱，存在或不存在所有基因组。该资料提供了不同蛋白质家族之间的功能链接信息。在另一种方法中，使用上述两种方法的组合来预测功能链接。

4. 发明授权

US06772069B1 Determining protein function and interaction from genome analysis 有权
标题翻译：确定蛋白质功能和基因组分析相互作用
公开(公告)号：US06772069B1
公开(公告)日：2004-08-03
申请号：US09493401
申请日：2000-01-28
申请人： David Eisenberg , Edward M. Marcotte , Michael J. Thompson , Matteo Pellegrini , Todd O. Yeates
发明人： David Eisenberg , Edward M. Marcotte , Michael J. Thompson , Matteo Pellegrini , Todd O. Yeates
IPC分类号： C12Q168
CPC分类号： G06F19/18 , G06F19/14 , G06F19/22
摘要： A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A′ and B′ have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A′ and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.
摘要翻译：提供了一种计算方法系统和计算机程序，用于从基因组序列推断功能链接。一种方法是基于一些观察结果，一些蛋白质A'和B'在另一个生物融合成单个蛋白质链AB的同源物。序列的跨基因组比较可以揭示这些AB序列，它们是Rosetta Stone序列，因为它们破译了A'和B之间的相互作用。另一种方法比较了两种或更多种生物体的基因组序列，以创建每种蛋白质的系统发育谱，存在或不存在所有基因组。该资料提供了不同蛋白质家族之间的功能链接信息。在另一种方法中，使用上述两种方法的组合来预测功能链接。

5. 发明授权

US06512981B1 Protein fold recognition using sequence-derived predictions 失效
标题翻译：蛋白质折叠识别使用序列导出的预测
公开(公告)号：US06512981B1
公开(公告)日：2003-01-28
申请号：US09071279
申请日：1998-05-01
申请人： David Eisenberg , Daniel Fischer
发明人： David Eisenberg , Daniel Fischer
IPC分类号： G06F1900
CPC分类号： G06F19/16 , G01N33/6803
摘要： A computer-assisted method for assigning an amino acid probe sequence to a known three-dimensional protein structure. In particular, the invention includes a method for using the amino acid sequence of a probe plus sequence-derived properties of the probe in making fold assignments. The method includes inputting into a computer system a string p1, p2 . . . pn describing the amino acid sequence of the probe sequence and at least one sequence-derived property for the probe sequence; inputting into a computer system a string t1, t2 . . . tm of structural properties for each member of a library of known 3D structures; executing an alignment algorithm in the computer to compute an alignment score indicating the optimal alignment of the string p1, p2 . . . pn to each string t1, t2 . . . tm by applying a combined compatibility function g(pi, tj); determining the statistical significance of each alignment score to determine a best-fit alignment score; and applying the best-fit alignment score to indicate or select the corresponding 3D protein structure from the library for output to a user. The invention includes a computer program implementation of such a method.
摘要翻译：用于将氨基酸探针序列分配给已知的三维蛋白质结构的计算机辅助方法。特别地，本发明包括使用探针的氨基酸序列加上探针的序列衍生性质进行折叠分配的方法。该方法包括向计算机系统输入字符串p1，p2。。。 pn描述探针序列的氨基酸序列和探针序列的至少一个序列衍生性质; 向计算机系统输入字符串t1，t2。。。已知3D结构库的每个成员的结构特性的tm; 在计算机中执行对准算法来计算指示字符串p1，p2的最佳对齐的对齐分数。。。 pn到每个字符串t1，t2。。。通过应用组合的兼容性函数g（pi，tj）; 确定每个比对得分的统计学显着性以确定最佳拟合比对得分; 并应用最佳拟合对准分数来指示或选择相应的3D蛋白质结构从库输出给用户。本发明包括这种方法的计算机程序实现。

6. 发明授权

US08692005B2 Catalyst for esteramine production 有权
标题翻译：酯胺生产催化剂
公开(公告)号：US08692005B2
公开(公告)日：2014-04-08
申请号：US13586023
申请日：2012-08-15
申请人： Marshall J. Nepras , Franz J. Luxem , Leonard F. Zaporowski , David Eisenberg
发明人： Marshall J. Nepras , Franz J. Luxem , Leonard F. Zaporowski , David Eisenberg
IPC分类号： C07C227/00
CPC分类号： C07C213/06 , B01J23/06 , B01J31/0227 , B01J31/04 , B01J2531/26 , C07C219/06 , C07C219/08
摘要： Provided are methods for decreasing the reaction time between an alkanolamine such as triethanolamine and a fatty acid alkyl ester such as, a triglyceride, a vegetable oil, a methyl ester, an ethyl ester, etc., a fatty acid, or a mixture thereof. The methods utilize a divalent zinc catalyst to facilitate and accelerate an esterification or transesterification reaction between the alkanolamine and the fatty acid, or fatty acid alkyl ester.
摘要翻译：提供了用于降低链烷醇胺如三乙醇胺和脂肪酸烷基酯如甘油三酯，植物油，甲酯，乙酯等，脂肪酸或其混合物之间的反应时间的方法。该方法利用二价锌催化剂来促进和加速链烷醇胺与脂肪酸或脂肪酸烷基酯之间的酯化反应或酯交换反应。

7. 发明申请

US20050209837A1 Bactericidal/permeability-increasing protein: crystallization, x-ray diffraction, three-dimensional structure determination, rational drug design and molecular modeling or related proteins 审中-公开
$Bactericidal/permeability-increasing protein: crystallization, x-ray diffraction, three-dimensional structure determination, rational drug design and molecular modeling or related proteins$
标题翻译：杀菌/渗透增加蛋白：结晶，x射线衍射，三维结构测定，合理药物设计和分子模拟或相关蛋白
公开(公告)号：US20050209837A1
公开(公告)日：2005-09-22
申请号：US10960853
申请日：2004-10-07
申请人： Lesa Beamer , Stephen Carroll , David Eisenberg
发明人： Lesa Beamer , Stephen Carroll , David Eisenberg
IPC分类号： G06G7/48 , G06G7/58
CPC分类号： C07K14/4742 , C07K2299/00 , G16B15/00
摘要： The present invention solves the three-dimensional structure of BPI and thereby provides atomic coordinates of BPI from the analysis of x-ray diffraction patterns of sufficiently high resolution for three-dimensional structure determination of the protein, as well as methods for rational drug design, based on using amino acid sequence data and/or x-ray diffraction data provided on computer readable media, as analyzed on a computer system having suitable computer algorithms; and atomic coordinates are provided yielding structural information on related proteins, including the lipid binding and lipid transport protein family that includes BPI, LBP, CETP and PLTP.
摘要翻译：本发明解决了BPI的三维结构，从而提供了足够高分辨率的x射线衍射图谱的分析用于蛋白质的三维结构测定的BPI的原子坐标，以及合理的药物设计方法，基于在具有合适的计算机算法的计算机系统上分析的使用在计算机可读介质上提供的氨基酸序列数据和/或x射线衍射数据; 并提供原子坐标，产生相关蛋白质的结构信息，包括脂质结合和脂质转运蛋白家族，包括BPI，LBP，CETP和PLTP。

8. 发明授权

US06680417B2 Oligomerization using a solid, unsupported metallocene catalyst system 有权
标题翻译：使用固体，未负载的茂金属催化剂体系进行低聚
公开(公告)号：US06680417B2
公开(公告)日：2004-01-20
申请号：US10037654
申请日：2002-01-03
申请人： Vahid Bagheri , Robert E. Farritor , Randall J. Stolk , Andrew D. Overstreet , David Eisenberg , Frederic Grzeszczak
发明人： Vahid Bagheri , Robert E. Farritor , Randall J. Stolk , Andrew D. Overstreet , David Eisenberg , Frederic Grzeszczak
IPC分类号： C07C226
CPC分类号： C07C2/34 , C07C2531/14 , C08F4/65912 , C08F4/65925 , C08F110/14
摘要： A process for the production of an oligomer oil by the polymerization of a feedstock containing one or more C3 to C20 1-olefins in the presence of a solid unsupported metallocene- and activator-containing catalyst system which is formed by removing the solvent from a solution of the soluble metallocene- and activator-containing catalyst system.
摘要翻译：在含有一种或多种C 3 -C 20 1-烯烃的原料的存在下，在固体无载体的含金属茂催化剂和活化剂的催化剂体系存在下，通过从溶液中除去溶剂而形成低聚物油的方法的可溶性茂金属和活化剂的催化剂体系。

9. 发明授权

US5917017A Diphtheria toxin vaccines bearing a mutated R domain 失效
标题翻译：具有突变的R结构域的白喉毒素疫苗
公开(公告)号：US5917017A
公开(公告)日：1999-06-29
申请号：US257781
申请日：1994-06-08
申请人： R. John Collier , Wei Hai Shen , David Eisenberg , Seunghyon Choe
发明人： R. John Collier , Wei Hai Shen , David Eisenberg , Seunghyon Choe
IPC分类号： C12N15/09 , A61K39/00 , A61K39/05 , A61K47/48 , A61P31/04 , C07H21/04 , C07K14/255 , C07K14/34 , C07K16/12 , C07K19/00 , C12N1/21 , C12P21/02 , C12P21/04 , C12P21/08 , C12R1/01 , C12R1/07 , C12R1/16 , C12R1/19 , C12R1/42 , C12R1/63 , C07K1/00 , A61K39/08
CPC分类号： C07K14/34 , A61K47/4833 , C07K16/12 , A61K39/00 , C07K2319/00
摘要： Diphtheria toxin polypeptides comprising a mutant R binding domain exhibit reduced target cell binding and may be used as vaccines to immunize a mammal against infection by Corynebacterium diphtheria.
摘要翻译：包含突变体R结合结构域的白喉毒素多肽表现出降低的靶细胞结合，并且可以用作免疫哺乳动物免受白喉棒状杆菌感染的疫苗。

10. 发明授权

US5843711A Diphtheria toxin receptor-binding region 失效
标题翻译：白喉毒素受体结合区
公开(公告)号：US5843711A
公开(公告)日：1998-12-01
申请号：US552248
申请日：1995-11-02
申请人： R. John Collier , David Eisenberg , Haian Fu , Seunghyon Choe
发明人： R. John Collier , David Eisenberg , Haian Fu , Seunghyon Choe
IPC分类号： C12N15/09 , A61K38/00 , A61K39/00 , A61K39/05 , A61P31/04 , C07H21/04 , C07K1/02 , C07K1/12 , C07K14/195 , C07K14/34 , C07K14/41 , C07K19/00 , C12N1/21 , C12P21/02 , C12R1/19 , C12N15/00
CPC分类号： C07K14/34 , A61K39/00 , C07K2319/00 , C07K2319/02 , C07K2319/55
摘要： The invention features a polypeptide consisting of amino acids 379-535 of diphtheria toxin, and portions thereof. This region, shown by X-ray crystallographic analysis to comprise the receptor binding domain of diphtheria toxin, is used as an immunogen and clinical therapeutic against diphtheria.
摘要翻译：本发明的特征在于由白喉毒素的氨基酸379-535组成的多肽及其部分。通过X射线晶体学分析显示的包含白喉毒素受体结合结构域的该区域被用作针对白喉的免疫原和临床治疗剂。

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