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    Directed protein docking algorithm
    4.
    发明申请
    Directed protein docking algorithm 审中-公开
    定向蛋白对接算法

    公开(公告)号：US20030215877A1

    公开(公告)日：2003-11-20

    申请号：US10407480

    申请日：2003-04-04

    Applicant: California Institute of Technology

    Inventor： John J. Love ,  Stephen L. Mayo

    IPC: G01N033/53 ,  G06G007/48 ,  G06G007/58 ,  G06F019/00 ,  G01N033/48 ,  G01N033/50 ,  C12P021/02 ,  C12N005/06

    CPC classification number: G01N33/6803 ,  G16B15/00 ,  G16B20/00

    Abstract: 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.

    Abstract translation: 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，蛋白质 - 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。

    Computationally targeted evolutionary design
    5.
    发明申请
    Computationally targeted evolutionary design 审中-公开
    计算目标进化设计

    公开(公告)号：US20010051855A1

    公开(公告)日：2001-12-13

    申请号：US09795500

    申请日：2001-02-16

    Applicant: California Institute of Technology

    Inventor： Zhen-Gang Wang ,  Christopher A. Voigt ,  Stephen L. Mayo ,  Frances H. Arnold

    IPC: G06F019/00 ,  G01N033/48 ,  G01N033/50

    CPC classification number: G16B15/00 ,  G16B20/00

    Abstract: 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 nullstructurally tolerantnull 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.

    Abstract translation: 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。

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