公开(公告)号：US10155943B2

公开(公告)日：2018-12-18

申请号：US14281421

申请日：2014-05-19

Applicant: Codexis, Inc.

Inventor： Richard Fox

IPC: C12N15/10 ,  C40B50/02 ,  G06F19/00 ,  G06N3/12 ,  G06F19/24

Abstract: The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.

公开(公告)号：US20180355514A1

公开(公告)日：2018-12-13

申请号：US15573352

申请日：2016-05-11

Applicant: Council of Scientific & Industrial Research

Inventor： Muthukumarasamy Karthikeyan ,  Deepak Karbhari Pandit

IPC: C40B30/02 ,  C40B50/02 ,  G06F19/00

CPC classification number: C40B30/02 ,  C40B50/02 ,  G06F19/701 ,  G06F19/708

Abstract: Method for encoding and decoding large scale molecular virtual libraries into a barcode Ligand-based drug discovery is often characterized with extraction of scaffolds, linkers and 5 building blocks from large small molecule datasets. Variable sites on scaffolds with attachment sites on building blocks participate in a combinatorial virtual reaction to generate a set of new virtual molecules. This process is time consuming and demands more storage space and is tedious to exchange data digitally. There is practically no quick way to sample molecules without enumerating the virtual library. Therefore, the present invention discloses a method of 10 encoding a virtual library of large scale molecular data into a single barcode. The present invention further discloses a method of decoding the barcode containing large scale data molecules.

公开(公告)号：US09864833B2

公开(公告)日：2018-01-09

申请号：US14256692

申请日：2014-04-18

Applicant: Codexis Mayflower Holdings, LLC

Inventor： Richard John Fox

IPC: G06F19/18 ,  C40B30/02 ,  C40B50/02 ,  C12N15/10 ,  G01N33/68 ,  G06F17/50 ,  G06N99/00 ,  G06F19/22 ,  G06F19/24

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.

公开(公告)号：US20170211206A1

公开(公告)日：2017-07-27

申请号：US15479220

申请日：2017-04-04

Applicant: Codexis, Inc.

Inventor： Gregory Allan Cope

IPC: C40B50/02 ,  G06F19/00 ,  G06F19/12 ,  G06F19/16 ,  G06F19/18

Abstract: The present invention provides methods for rapidly and efficiently searching biologically-related data space. More specifically, the present invention provides methods for 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 present invention also provides methods for modeling sequence-activity relationships, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods. The present invention further provides digital systems and software for performing the methods provided herein.

公开(公告)号：US09354228B2

公开(公告)日：2016-05-31

申请号：US13810570

申请日：2011-07-14

Applicant: Maximiliano Vasquez ,  Arvind Sivasubramanian ,  Michael Feldhaus

Inventor： Maximiliano Vasquez ,  Arvind Sivasubramanian ,  Michael Feldhaus

IPC: C40B40/08 ,  G01N33/543 ,  C07K16/00 ,  C12N15/10 ,  C40B50/02

CPC classification number: C12N15/1089 ,  C07K16/00 ,  C07K2317/21 ,  C07K2317/565 ,  C07K2317/567 ,  C40B40/08 ,  C40B50/02 ,  C40B50/06 ,  G01N33/543

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity.

Abstract translation: 本发明克服了通过专门设计具有定向序列和长度多样性的文库来生成抗体编码多核苷酸文库的已知方法中的不足之处。

公开(公告)号：US20150110836A1

公开(公告)日：2015-04-23

申请号：US14398084

申请日：2013-05-21

Applicant: DISTRIBUTED BIO, INC.

Inventor： Jacob E. Glanville

IPC: C07K14/005 ,  C12N7/00 ,  G06F19/22 ,  G06F19/18 ,  C40B50/02 ,  A61K39/21 ,  A61K38/46

CPC classification number: C07K14/005 ,  A61K38/46 ,  A61K39/0011 ,  A61K39/12 ,  A61K39/21 ,  A61K2039/515 ,  A61K2039/5154 ,  A61K2039/53 ,  A61K2039/575 ,  A61K2039/70 ,  C12N7/00 ,  C12N2740/16034 ,  C12N2740/16071 ,  C12N2740/16122 ,  C12N2740/16134 ,  C12N2760/16122 ,  C12N2760/16134 ,  C12Y306/05002 ,  C40B50/02 ,  G06F19/18 ,  G06F19/22

Abstract: The present disclosure provides compositions and methods for the generation of an antibody or immunogenic composition, such as a vaccine, through epitope focusing by variable effective antigen surface concentration. Generally, the composition and methods of the disclosure comprise three steps: a “design process” comprising one or more in silico bioinformatics steps to select and generate a library of potential antigens for use in the immunogenic composition; a “formulation process”, comprising in vitro testing of potential antigens, using various biochemical assays, and further combining two or more antigens to generate one or more immunogenic compositions; and an “administering” step, whereby the immunogenic composition is administered to a host animal, immune cell, subject or patient. Further steps may also be included, such as the isolation and production of antibodies raised by host immune response to the immunogenic composition.

Abstract translation: 本公开提供了通过可变有效抗原表面浓度的表位聚焦来产生抗体或免疫原性组合物如疫苗的组合物和方法。 通常，本公开的组合物和方法包括三个步骤：包含一个或多个计算机生物信息学步骤的“设计过程”，以选择和产生用于免疫原性组合物的潜在抗原文库; 包括使用各种生化测定法进行潜在抗原的体外测试，以及进一步组合两种或多种抗原以产生一种或多种免疫原性组合物的“制剂方法” 和“施用”步骤，由此将免疫原性组合物施用于宿主动物，免疫细胞，受试者或患者。 还可以包括进一步的步骤，例如由免疫原性组合物的宿主免疫应答产生的抗体的分离和产生。

公开(公告)号：US20130059296A1

公开(公告)日：2013-03-07

申请号：US13592827

申请日：2012-08-23

Applicant: Joseph Jacobson ,  Daniel Schindler ,  Scott S. Lawton

Inventor： Joseph Jacobson ,  Daniel Schindler ,  Scott S. Lawton

IPC: C12P19/34 ,  C40B60/14 ,  C40B40/06 ,  C12Q1/68 ,  C40B50/02

CPC classification number: C12N15/66 ,  C12N15/10 ,  C12N15/1027 ,  C12N15/1031 ,  C12N15/1089 ,  C12P19/34 ,  C12Q2521/301 ,  C12Q2521/501 ,  G16B30/00

Abstract: Aspects of the invention relate to methods, compositions and algorithms for designing and producing a target nucleic acid. The method can include: (1) providing a plurality of blunt-end double-stranded nucleic acid fragments having a restriction enzyme recognition sequence at both ends thereof; (2) producing via enzymatic digestion a plurality of cohesive-end double-stranded nucleic acid fragments each having two different and non-complementary overhangs; (3) ligating the plurality of cohesive-end double-stranded nucleic acid fragments with a ligase; and (4) forming a linear arrangement of the plurality of cohesive-end double-stranded nucleic acid fragments, wherein the unique arrangement comprises the target nucleic acid. In certain embodiments, the plurality of blunt-end double-stranded nucleic acid fragments can be provided by: releasing a plurality of oligonucleotides synthesized on a solid support; and synthesizing complementary strands of the plurality of oligonucleotides using a polymerase based reaction.

Abstract translation: 本发明的方面涉及用于设计和产生靶核酸的方法，组合物和算法。 该方法可以包括：（1）提供多个在其两端具有限制酶识别序列的平末端双链核酸片段; （2）通过酶消化产生多个具有两个不同和非互补突出端的粘性末端双链核酸片段; （3）用连接酶连接多个内聚端双链核酸片段; 和（4）形成多个内聚端双链核酸片段的线性排列，其中独特的排列包含靶核酸。 在某些实施方案中，多个平末端双链核酸片段可以通过以下方式提供：释放在固体支持物上合成的多种寡核苷酸; 并使用基于聚合酶的反应合成多个寡核苷酸的互补链。

公开(公告)号：US20110257044A1

公开(公告)日：2011-10-20

申请号：US12316675

申请日：2008-12-16

Applicant: Peizhi Luo ,  Mark Hsieh

Inventor： Peizhi Luo ,  Mark Hsieh

IPC: C40B50/02 ,  G06F19/10 ,  C40B50/06

CPC classification number: C40B40/10 ,  B01J2219/00689 ,  B01J2219/00695 ,  B01J2219/007 ,  B01J2219/00725 ,  C07K16/00 ,  C07K2299/00 ,  C07K2317/21 ,  C07K2317/24 ,  C07K2317/622 ,  C07K2319/00 ,  C12N15/1089 ,  G16B35/00 ,  G16C20/60

Abstract: Methods and systems are provided for constructing recombinant antibody libraries based on three-dimensional structures of antibodies from various species including human. In one aspect, a library of antibodies with diverse sequences is efficiently constructed in silico to represent the structural repertoire of the vertebrate antibodies. Such a functionally representative library provides a structurally diverse and yet functionally more relevant source of antibody candidates which can then be screened for high affinity binding to a wide variety of target molecules, including but not limited to biomacromolecules such as protein, peptide, and nucleic acids, and small molecules.

Abstract translation: 提供了基于来自包括人在内的各种物种的抗体的三维结构构建重组抗体文库的方法和系统。 在一个方面，具有不同序列的抗体文库有效地构建成计算机以表示脊椎动物抗体的结构谱。 这样的功能代表性的文库提供了结构上多样但功能上更相关的抗体候选来源，然后可以筛选其与多种靶分子的高亲和力结合，包括但不限于生物大分子如蛋白质，肽和核酸 ，和小分子。

公开(公告)号：US20110034342A1

公开(公告)日：2011-02-10

申请号：US12867433

申请日：2009-02-12

Applicant: Richard Fox

Inventor： Richard Fox

IPC: C40B30/00 ,  C40B50/02 ,  C40B60/14 ,  C40B40/00

CPC classification number: C12N15/1089 ,  C12N15/1058 ,  C40B50/02 ,  G06F19/24 ,  G06F19/707 ,  G06N3/126

Abstract: The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.

Abstract translation: 本公开涉及一种产生不同组的变体以筛选变体群体内的改进和新颖性质的方法，用于产生不同变体组的系统和变体肽。

公开(公告)号：US20100292131A1

公开(公告)日：2010-11-18

申请号：US12742647

申请日：2008-11-12

Applicant: Koen Kas ,  Griet Vanpoucke ,  Sven Degroeve ,  Kathleen Huijben

Inventor： Koen Kas ,  Griet Vanpoucke ,  Sven Degroeve ,  Kathleen Huijben

IPC: A61K38/00 ,  C40B30/04 ,  C40B40/10 ,  C40B50/02 ,  G01N33/53 ,  A61P5/00

CPC classification number: G01N33/6893 ,  C07K17/02 ,  G01N2800/26 ,  G01N2800/50 ,  G01N2800/52

Abstract: The present invention provides kits and methods for the diagnosis, prognosis and prediction of sepsis in a subject or for the differentiation between sepsis and SIRS in a subject, the method comprising(a) measuring the level of pro-hepcidin (pro-HEPC) in a biological sample taken from said subject, (b) measuring the level of at least one further biomarker selected from the group consisting of soluble TNF-receptor 2 (sTNFR2), Pentraxin-3 (PTX-3), Macrophage Colony-Stimulating Factor (MCSF), pro-Brain Natriuretic Protein (pro-BNP), one or more members of the Histone protein family, Procalcitonin (PCT) and c-Reactive Protein (CRP) in a biological sample from said subject, (c) using said measurements obtained in steps (a) and (b) to create a profile for said biomarkers and (d) comparing said profile with a reference biomarker profile obtained form a patient having SIRS or from a healthy subject.

Abstract translation: 本发明提供了用于诊断，预后和预测受试者中败血症或受试者中脓毒症和SIRS之间的分化的试剂盒和方法，所述方法包括（a）测量前体铁调素（pro-hepcidin） 从所述对象获取的生物样品，（b）测量至少一种选自下组的生物标志物的水平：可溶性TNF-受体2（sTNFR2），Pentraxin-3（PTX-3），巨噬细胞集落刺激因子 MCSF），前脑利钠蛋白（pro-BNP），组蛋白家族中的一个或多个成员，来自所述受试者的生物样品中的降钙素原（PCT）和C-反应蛋白（CRP），（c）使用所述测量 在步骤（a）和（b）中获得以产生用于所述生物标志物的分布图，（d）将所述分布与从具有SIRS或健康受试者的患者获得的参考生物标志物概况进行比较。