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    Universal Fibronectin Type III Bottom-Side Binding Domain Libraries
    2.
    发明申请
    Universal Fibronectin Type III Bottom-Side Binding Domain Libraries 审中-公开
    通用纤连蛋白III型底部结合域文库

    公开(公告)号：US20160194626A1

    公开(公告)日：2016-07-07

    申请号：US14828763

    申请日：2015-08-18

    Applicant: Andreas LOEW ,  Brian VASH

    Inventor： Andreas LOEW ,  Brian VASH

    IPC: C12N15/10 ,  G01N33/566

    CPC classification number: C12N15/1037 ,  C12N15/1044 ,  C40B30/02 ,  C40B40/10 ,  C40B50/02 ,  G01N33/566 ,  G06F19/16

    Abstract: The invention pertains to a natural-variant combinatorial library of fibronectin Type 3 domain (Fn3) polypeptides useful in screening for the presence of one or more polypeptides having a selected binding or enzymatic activity. The library polypeptides include (a) regions A, AB, B, C, CD, D, E, EF, F, and G having wildtype amino acid sequences of a selected native fibronectin Type 3 polypeptide or polypeptides, and (b) loop regions AB, CD, and EF having selected lengths (Bottom Loops). The Fn3 may also have loop regions BC, DE, and FG having wildtype amino acid sequences, having selected lengths, or mutagenized amino acid sequences (Top Loops).

    Abstract translation: 本发明涉及可用于筛选具有选定结合或酶活性的一种或多种多肽的存在的纤连蛋白3型结构域（Fn3）多肽的天然变体组合文库。 文库多肽包括（a）具有所选天然纤连蛋白3型多肽或多肽的野生型氨基酸序列的区域A，AB，B，C，CD，D，E，EF，F和G，和（b）环区 AB，CD和EF，具有选定的长度（底部循环）。 Fn3还可以具有具有野生型氨基酸序列，具有选定长度或诱变的氨基酸序列（Top Loops）的环区BC，DE和FG。

    METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIO-MOLECULES
    4.
    发明申请
    METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIO-MOLECULES 审中-公开
    用于鉴定功能性生物分子的方法，系统和软件

    公开(公告)号：US20140249035A1

    公开(公告)日：2014-09-04

    申请号：US14256692

    申请日：2014-04-18

    Applicant: Codexis Mayflower Holdings, LLC

    Inventor： Richard John Fox

    IPC: G06F19/18 ,  C12N15/10

    CPC classification number: G06F19/18 ,  C12N15/1058 ,  C40B30/02 ,  C40B50/02 ,  G01N33/6818 ,  G06F17/50 ,  G06F19/22 ,  G06F19/24 ,  G06N99/005

    Abstract: 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.

    Abstract translation: 本发明一般涉及快速有效地搜索生物相关数据空间的方法。 更具体地，本发明包括从复杂的生物分子文库或这些文库集合鉴定具有所需性质或最适合于获得这些性质的生物分子的方法。 本发明还提供了对序列活性关系建模的方法。 由于许多方法是计算机实现的，本发明另外提供用于执行这些方法的数字系统和软件。

    Methods and Systems for Genetic Analysis
    5.
    发明申请
    Methods and Systems for Genetic Analysis 有权
    遗传分析方法与系统

    公开(公告)号：US20140200147A1

    公开(公告)日：2014-07-17

    申请号：US14141990

    申请日：2013-12-27

    Applicant: Personalis, Inc.

    Inventor： Gabor T. Bartha ,  Gemma Chandratillake ,  Richard Chen ,  Sarah Garcia ,  Hugo Yu Kor Lam ,  Shujun Luo ,  Mark R. Pratt ,  John West

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C40B50/02 ,  G06F19/10 ,  G06F19/18 ,  G06F19/22

    Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

    Abstract translation: 本公开提供了用于样本处理和数据分析的系统和方法。 样品处理可包括核酸样品处理和随后的测序。 可以对核酸样品中的一些或全部进行测序以提供可存储或以其他方式保存在电子存储位置中的序列信息。 可以借助于计算机处理器来分析序列信息，并且所分析的序列信息可以存储在电子存储位置中，该电子存储位置可以包括从核酸样品产生的序列信息和分析的序列信息的集合或集合。 本公开的方法和系统可用于例如核酸样品的分析，用于产生一个或多个文库以及用于生产生物医学报告。 本公开的方法和系统可以帮助诊断，监测，治疗和预防一种或多种疾病和病症。

    METHOD OF GENERATING AN OPTIMIZED, DIVERSE POPULATION OF VARIANTS
    7.
    发明申请
    METHOD OF GENERATING AN OPTIMIZED, DIVERSE POPULATION OF VARIANTS 有权
    生成优化的多样化人口变化的方法

    公开(公告)号：US20110029468A1

    公开(公告)日：2011-02-03

    申请号：US12867429

    申请日：2009-02-12

    Applicant: Richard Fox

    Inventor： Richard Fox

    IPC: G06N3/12

    CPC classification number: C40B50/02 ,  G06F19/24 ,  G06N3/126

    Abstract: The present disclosure relates to methods of rapidly and efficiently searching biologically-related data space to identify a population set maximally diverse and optimized for sets of desired properties. More specifically, the disclosure provides methods of identifying a diverse, evolutionary separated bio-molecules with desired properties from complex bio-molecule libraries. The disclosure additionally provides digital systems and software for performing these methods.

    Abstract translation: 本公开涉及快速有效地搜索生物相关数据空间的方法，以识别针对所需属性的集合最大程度地多样化和优化的群体集合。 更具体地，本公开提供了鉴定来自复杂生物分子文库的具有所需性质的多种，进化分离的生物分子的方法。 本公开另外提供用于执行这些方法的数字系统和软件。

    Computer based method for identifying peptides useful as drug targets
    9.
    发明授权
    Computer based method for identifying peptides useful as drug targets 有权
    用于鉴定可用作药物靶标的肽的基于计算机的方法

    公开(公告)号：US07657378B1

    公开(公告)日：2010-02-02

    申请号：US09539032

    申请日：2000-03-30

    Applicant: Samir Kumar Brahmachari ,  Debasis Dash

    Inventor： Samir Kumar Brahmachari ,  Debasis Dash

    IPC: G06F19/00

    CPC classification number: C40B50/02 ,  C07K1/00 ,  C07K14/195 ,  G06F19/18 ,  G06F19/22

    Abstract: 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.

    Abstract translation: 本发明涉及一种用于进行几种生物体的基因组方式比较的基于计算机的方法，所述计算方法包括从几种生物体的蛋白质序列产生肽文库，随后进行比较，导致保守的不变肽基序的鉴定，并且对此 已经通过各种细菌生物体和宿主基因组之间的直接序列比较来确定几个不变的肽基序，而没有任何先验假设，本方法可用于鉴定潜在的药物靶标，并且可以作为广谱抗菌药物的筛选 对于感染的特异性诊断，另外还借助于这种不变的肽基序签名来赋予功能至尚未知功能的蛋白质。

    Methods and apparatus for preparing high-dimensional combinatorial experiments
    10.
    发明申请
    Methods and apparatus for preparing high-dimensional combinatorial experiments 失效
    制备高维组合实验的方法和装置

    公开(公告)号：US20070214101A1

    公开(公告)日：2007-09-13

    申请号：US11348873

    申请日：2006-02-06

    Applicant: Youqi Wang ,  Marco Falcioni ,  Stephen Turner ,  C. Ramberg

    Inventor： Youqi Wang ,  Marco Falcioni ,  Stephen Turner ,  C. Ramberg

    IPC: G06N5/00

    CPC classification number: C40B50/02 ,  B01J2219/00605 ,  B01J2219/00621 ,  B01J2219/00659 ,  B01J2219/00689 ,  B01J2219/00695 ,  B01J2219/007

    Abstract: 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.

    Abstract translation: 包括计算机程序设备在内的计算机实现的方法，系统和装置提供了用于设计要用一组资源执行的一组实验的技术。 基于描述在实验中变化的因素的一组参数生成多个实验配置，以及一组表示可以用该组资源执行的操作的限制。 基于所选配置定义一组实验。 约束可以表示为将参数应用于实验网格的一个或多个点的集合的模式。

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