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1. 发明申请

WO2003087310A3 DIRECTED PROTEIN DOCKING ALGORITHM 审中-公开
公开(公告)号：WO2003087310A3
公开(公告)日：2003-10-23
申请号：PCT/US2003/010535
申请日：2003-04-04
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , LOVE, John, J. , MAYO, Stephen, L.
发明人： LOVE, John, J. , MAYO, Stephen, L.
IPC分类号： G01N33/68
摘要： The instant invention provides methods and computational tools for designing interaction between molecules based on their three-dimensional atomic coordinates. In a preferred embodiment, the method can be used to design protein-protein interactions based on their three-dimensional structure. In one embodiment, the method of the instant invention includes a first step of docking interacting molecules based on their surface geometric fit by quantitative correlation techniques, followed by a second step of optimizing the resulting interacting surface by altering interface side-chains, such that the interfacial side-chains are repacked in a manner analogous to the cores of well-folded proteins. The method can be used in numerous applications, including redesigning interaction interfaces between known protein-protein, protein-polynucleotide, protein-carbohydrates (such as polysaccharide), protein-lipid (or steroid), enzyme-inhibitor, or antibody-target epitope pairs, or rational design of more potent drug molecules.

2. 发明申请

WO03073238A2 COMPUTATIONAL METHOD FOR DESIGNING ENZYMES FOR INCORPORATION OF AMINO ACID ANALOGS INTO PROTEINS 审中-公开
标题翻译：用于将氨基酸类似物加入蛋白质的酶的设计方法
公开(公告)号：WO03073238A2
公开(公告)日：2003-09-04
申请号：PCT/US0306083
申请日：2003-02-27
申请人： CALIFORNIA INST OF TECHN , DATTA DEEPSHIKHA , WANG PIN , CARRICO ISAAC , MAYO STEPHEN L , TIRRELL DAVID
发明人： DATTA DEEPSHIKHA , WANG PIN , CARRICO ISAAC , MAYO STEPHEN L , TIRRELL DAVID
IPC分类号： C07K1/00 , C12N5/06 , C12N9/00 , C12N9/22 , C12N15/00 , C12P21/02 , G01N33/48 , G01N33/50 , G06F19/16 , G06F
CPC分类号： C12N9/93 , C07K1/00 , C07K2299/00 , G06F19/16
摘要： The instant invention provides methods, reagents, and computational tools for designing non-natural substrate analogs for enzymes, especially for designing unnatural amino acid analogs for aminoacyl tRNA Synthetases (AARSs), such as the Phe tRNA Synthetase. The instant invention also provides methods to incorporate unnatural amino acid analogs, especially those with interesting functional groups, into protein products to generate proteins of modified or novel functions.
摘要翻译：本发明提供了用于设计用于酶的非天然底物类似物的方法，试剂和计算工具，特别是用于设计用于氨基tRNA合成酶（AARS）的非天然氨基酸类似物，例如Phe tRNA合成酶。本发明还提供了将非天然氨基酸类似物（特别是那些具有感兴趣的官能团的类似物）掺入蛋白质产物以产生修饰或新颖功能的蛋白质的方法。

3. 发明申请

WO2003091835A3 COMPUTATIONALLY TARGETED EVOLUTIONARY DESIGN 审中-公开
公开(公告)号：WO2003091835A3
公开(公告)日：2003-11-06
申请号：PCT/US2002/034342
申请日：2002-10-25
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
发明人： VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
IPC分类号： G06F19/00
摘要： The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying "structurally tolerant" residues of a polymer. Mutations of these, structurally tolerant residues are less likely to adversely affect desirable properties of a polymer sequence. The invention further provides improved methods for directed evolution wherein the structurally tolerant residues of a polymer are selectively mutated. Computer systems for implementing analytical methods of the invention are also provided.

4. 发明申请

WO2003091835A2 COMPUTATIONALLY TARGETED EVOLUTIONARY DESIGN 审中-公开
标题翻译：计算方向的演进设计
公开(公告)号：WO2003091835A2
公开(公告)日：2003-11-06
申请号：PCT/US2002/034342
申请日：2002-10-25
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
发明人： VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
IPC分类号： G06F
CPC分类号： G06F19/16 , G06F19/18
摘要： The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying "structurally tolerant" residues of a polymer. Mutations of these, structurally tolerant residues are less likely to adversely affect desirable properties of a polymer sequence. The invention further provides improved methods for directed evolution wherein the structurally tolerant residues of a polymer are selectively mutated. Computer systems for implementing analytical methods of the invention are also provided.
摘要翻译：本发明涉及聚合物定向进化的改进方法，包括核酸和蛋白质的定向进化。具体地，本发明的方法包括用于鉴定聚合物的“结构上耐受性”残留物的分析方法。这些结构上耐受性残基的突变不太可能不利地影响聚合物序列的期望性质。本发明还提供了用于定向进化的改进方法，其中聚合物的结构耐受性残基被选择性突变。还提供了用于实现本发明的分析方法的计算机系统。

5. 发明申请

WO2003073238A3 COMPUTATIONAL METHOD FOR DESIGNING ENZYMES FOR INCORPORATION OF AMINO ACID ANALOGS INTO PROTEINS 审中-公开
公开(公告)号：WO2003073238A3
公开(公告)日：2003-09-04
申请号：PCT/US2003/006083
申请日：2003-02-27
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , DATTA, Deepshikha , WANG, Pin , CARRICO, Isaac , MAYO, Stephen, L. , TIRRELL, David
发明人： DATTA, Deepshikha , WANG, Pin , CARRICO, Isaac , MAYO, Stephen, L. , TIRRELL, David
IPC分类号： G01N31/00
摘要： The instant invention provides methods, reagents, and computational tools for designing non-natural substrate analogs for enzymes, especially for designing unnatural amino acid analogs for aminoacyl tRNA Synthetases (AARSs), such as the Phe tRNA Synthetase. The instant invention also provides methods to incorporate unnatural amino acid analogs, especially those with interesting functional groups, into protein products to generate proteins of modified or novel functions.

6. 发明申请

WO03087310A2 DIRECTED PROTEIN DOCKING ALGORITHM 审中-公开
标题翻译：指导蛋白质锁定算法
公开(公告)号：WO03087310A2
公开(公告)日：2003-10-23
申请号：PCT/US0310535
申请日：2003-04-04
申请人： CALIFORNIA INST OF TECHN , LOVE JOHN J , MAYO STEPHEN L
发明人： LOVE JOHN J , MAYO STEPHEN L
IPC分类号： G01N33/68 , G06F19/16 , G06F19/18 , C12N
CPC分类号： G06F19/16 , G01N33/6803 , G06F19/18
摘要： The instant invention provides methods and computational tools for designing interaction between molecules based on their three-dimensional atomic coordinates. In a preferred embodiment, the method can be used to design protein-protein interactions based on their three-dimensional structure. In one embodiment, the method of the instant invention includes a first step of docking interacting molecules based on their surface geometric fit by quantitative correlation techniques, followed by a second step of optimizing the resulting interacting surface by altering interface side-chains, such that the interfacial side-chains are repacked in a manner analogous to the cores of well-folded proteins. The method can be used in numerous applications, including redesigning interaction interfaces between known protein-protein, protein-polynucleotide, protein-carbohydrates (such as polysaccharide), protein-lipid (or steroid), enzyme-inhibitor, or antibody-target epitope pairs, or rational design of more potent drug molecules.
摘要翻译：本发明提供了用于基于它们的三维原子坐标来设计分子之间的相互作用的方法和计算工具。在优选的实施方案中，该方法可用于基于其三维结构设计蛋白质 - 蛋白质相互作用。在一个实施方案中，本发明的方法包括通过定量相关技术基于其表面几何拟合对接相互作用分子的第一步骤，随后是通过改变界面侧链优化所得到的相互作用表面的第二步骤，使得界面侧链以类似于良好折叠蛋白质核心的方式重新包装。该方法可用于许多应用，包括重新设计已知蛋白质 - 蛋白质，蛋白质 - 多核苷酸，蛋白 - 碳水化合物（如多糖），蛋白质 - 脂质（或类固醇），酶抑制剂或抗体 - 靶标表位对之间的相互作用界面，或合理设计更有效的药物分子。

7. 发明申请

WO0190346A3 GENE RECOMBINATION AND HYBRID PROTEIN DEVELOPMENT 审中-公开
标题翻译：基因重组和杂交蛋白质的开发
公开(公告)号：WO0190346A3
公开(公告)日：2002-10-10
申请号：PCT/US0116831
申请日：2001-05-23
申请人： CALIFORNIA INST OF TECHN , WANG ZHEN-GANG , VOIGT CHRISTOPHER A , MAYO STEPHEN L , ARNOLD FRANCES H
发明人： WANG ZHEN-GANG , VOIGT CHRISTOPHER A , MAYO STEPHEN L , ARNOLD FRANCES H
IPC分类号： C12N15/10 , G06F19/22 , G06F17/50 , G06F19/00
CPC分类号： G06F19/14 , C12N15/1027 , G06F19/22
摘要： The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying "crossover locations" in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified "crossover locations". Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations. Computer systems for implementing analytical methods of the invention are also provided.
摘要翻译：本发明涉及聚合物定向进化的改进方法，包括核酸和蛋白质的定向进化。具体地，本发明的方法包括用于识别聚合物中的“交叉位置”的分析方法。这些位置处的交叉链不太可能破坏蛋白质的所需性质，例如稳定性或功能性。本发明还提供了用于定向进化的改进方法，其中聚合物在所识别的“交叉位置”选择性重组。交叉中断配置文件可用于标识首选交叉位置。还可以鉴定和分析生物聚合物的结构域，并将结构域组织成模式。可以例如基于构象能量或原子间距离来计算模式中断简档，并且这些可以用于识别优选或候选交叉位置。还提供了用于实现本发明的分析方法的计算机系统。

8. 发明申请

WO2003055978A3 GENE RECOMBINATION AND HYBRID PROTEIN DEVELOPMENT 审中-公开
公开(公告)号：WO2003055978A3
公开(公告)日：2003-07-10
申请号：PCT/US2002/034374
申请日：2002-10-25
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
发明人： VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
IPC分类号： G01N33/48
摘要： The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying "crossover locations" in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified "crossover locations". Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations. Computer systems for implementing analytical methods of the invention are also provided.

9. 发明申请

WO2003055978A2 GENE RECOMBINATION AND HYBRID PROTEIN DEVELOPMENT 审中-公开
标题翻译：基因重组和杂交蛋白质的开发
公开(公告)号：WO2003055978A2
公开(公告)日：2003-07-10
申请号：PCT/US2002/034374
申请日：2002-10-25
申请人： CALIFORNIA INSTITUTE OF TECHNOLOGY , VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
发明人： VOIGT, Christopher, A. , WANG, Zhen-Gang , ARNOLD, Frances, H. , MAYO, Stephen, L.
IPC分类号： C12N
CPC分类号： G06F19/14 , C12N15/1027 , G06F19/22
摘要： The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying "crossover locations" in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified "crossover locations". Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations. Computer systems for implementing analytical methods of the invention are also provided.
摘要翻译：本发明涉及聚合物定向进化的改进方法，包括核酸和蛋白质的定向进化。具体地，本发明的方法包括用于识别聚合物中的“交叉位置”的分析方法。这些位置处的交叉链不太可能破坏蛋白质的所需性质，例如稳定性或功能性。本发明还提供了用于定向进化的改进方法，其中聚合物在所识别的“交叉位置”选择性重组。交叉中断配置文件可用于标识首选交叉位置。还可以鉴定和分析生物聚合物的结构域，并将结构域组织成模式。可以例如基于构象能量或原子间距离来计算模式中断简档，并且这些可以用于识别优选或候选交叉位置。还提供了用于实现本发明的分析方法的计算机系统。

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