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    Method and system for designing proteins and protein backbone configurations
    1.
    发明申请
    Method and system for designing proteins and protein backbone configurations 审中-公开

    公开(公告)号：US20070027633A1

    公开(公告)日：2007-02-01

    申请号：US11528975

    申请日：2006-09-27

    申请人： Jonathan Miller ,  Chen Zeng

    发明人： Jonathan Miller ,  Chen Zeng

    IPC分类号： G06F19/00

    CPC分类号： G16B15/00 ,  G16B30/00

    摘要： The present invention provides a method and system for identifying, designing, and synthesizing proteins and protein backbones. The invention permits the qualitative identification of designable protein configurations and synthesis of protein folds. The method and system involve generating backbone protein configurations using a set of dihedral angle pairs, normalizing the total surface exposure of the configurations; generating a random set of sequences of hydrophobicities with uniform weight on the space of allowed sequences; determining, for each randomly generated sequence, which of the remaining configurations is the ground state; recording a ground-state configuration for each sequence wherein the desirable configurations are those containing the most sequences with that configuration as their ground state and finally, synthesizing sequences of amino acids for the desirable configurations.

    Method and system for designing proteins and protein backbone configurations
    2.
    发明申请
    Method and system for designing proteins and protein backbone configurations 审中-公开
    设计蛋白质和蛋白质骨架配置的方法和系统

    公开(公告)号：US20070032962A1

    公开(公告)日：2007-02-08

    申请号：US11528987

    申请日：2006-09-27

    申请人： Jonathan Miller ,  Chen Zeng ,  Ned Wingreen ,  Chao Tang

    发明人： Jonathan Miller ,  Chen Zeng ,  Ned Wingreen ,  Chao Tang

    IPC分类号： G06F19/00

    CPC分类号： G16B15/00 ,  G16B30/00

    摘要： The present invention provides a method and system for identifying, designing, and synthesizing proteins and protein backbones. The invention permits the qualitative identification of designable protein configurations and synthesis of protein folds. The method and system involve generating backbone protein configurations using a set of dihedral angle pairs, normalizing the total surface exposure of the configurations; generating a random set of sequences of hydrophobicities with uniform weight on the space of allowed sequences; determining, for each randomly generated sequence, which of the remaining configurations is the ground state; recording a ground-state configuration for each sequence wherein the desirable configurations are those containing the most sequences with that configuration as their ground state and finally, synthesizing sequences of amino acids for the desirable configurations.

    摘要翻译： 本发明提供了鉴定，设计和合成蛋白质和蛋白质主链的方法和系统。 本发明允许定性鉴定可设计的蛋白质构型和蛋白质折叠的合成。 该方法和系统包括使用一组二面角对产生骨架蛋白构型，使构型的总表面暴露标准化; 在允许的序列的空间上产生具有均匀重量的疏水性序列的随机集合; 为每个随机生成的序列确定剩余配置中的哪一个是基态; 记录每个序列的基态配置，其中期望的配置是那些包含具有该构型的最多序列作为其基础状态的配置，最后合成用于期望配置的氨基酸序列。

    Method and system for designing proteins and protein backbone configurations
    3.
    发明申请
    Method and system for designing proteins and protein backbone configurations 审中-公开

    公开(公告)号：US20070021926A1

    公开(公告)日：2007-01-25

    申请号：US11528974

    申请日：2006-09-27

    申请人： Jonathan Miller ,  Chen Zeng ,  Ned Wingreen ,  Chao Tang

    发明人： Jonathan Miller ,  Chen Zeng ,  Ned Wingreen ,  Chao Tang

    IPC分类号： G06F19/00

    CPC分类号： G16B15/00 ,  G16B30/00

    摘要： The present invention provides a method and system for identifying, designing, and synthesizing proteins and protein backbones. The invention permits the qualitative identification of designable protein configurations and synthesis of protein folds. The method and system involve generating backbone protein configurations using a set of dihedral angle pairs, normalizing the total surface exposure of the configurations; generating a random set of sequences of hydrophobicities with uniform weight on the space of allowed sequences; determining, for each randomly generated sequence, which of the remaining configurations is the ground state; recording a ground-state configuration for each sequence wherein the desirable configurations are those containing the most sequences with that configuration as their ground state and finally, synthesizing sequences of amino acids for the desirable configurations.

    SYSTEM AND METHOD FOR OBTAINING INFORMATION ABOUT BIOLOGICAL NETWORKS USING A LOGIC BASED APPROACH
    4.
    发明申请
    SYSTEM AND METHOD FOR OBTAINING INFORMATION ABOUT BIOLOGICAL NETWORKS USING A LOGIC BASED APPROACH 审中-公开
    使用基于逻辑的方法获取关于生物网络的信息的系统和方法

    公开(公告)号：US20100299289A1

    公开(公告)日：2010-11-25

    申请号：US12783849

    申请日：2010-05-20

    申请人： Rahul SIMHA ,  Guanyu Wang ,  Chen Zeng

    发明人： Rahul SIMHA ,  Guanyu Wang ,  Chen Zeng

    IPC分类号： G06F15/18 ,  G06F17/11

    CPC分类号： G16B5/00

    摘要： A system and method of obtaining information concerning the structure-function relationship of biological networks can be studied holistically through the ensemble characterization of all the networks that realize a given biological function. A logic-based approach enables significant advances in computability and concept development (minimality and reducibility). The approach is applied to a biologically relevant trajectory and reveals some interesting properties. By using the approach, a cell cycle network is decomposed into three components with the functioning of each component explained.

    摘要翻译： 可以通过实现给定生物学功能的所有网络的整体表征来整体地研究获得关于生物网络的结构 - 功能关系的信息的系统和方法。 基于逻辑的方法可以显着提高可计算性和概念开发（最低限度和可缩减性）。 该方法应用于生物相关的轨迹，并揭示一些有趣的属性。 通过使用该方法，细胞周期网络被分解为三个组件，并且解释每个组件的功能。