公开(公告)号：US10025900B2

公开(公告)日：2018-07-17

申请号：US14776532

申请日：2014-03-14

Applicant: Alexandre Zanghellini ,  Yih-En Andrew Ban ,  Eric Anthony Althoff ,  Daniela Grabs ,  Mihai Luchian Azoitei

Inventor： Alexandre Zanghellini ,  Yih-En Andrew Ban ,  Eric Anthony Althoff ,  Daniela Grabs ,  Mihai Luchian Azoitei

IPC: C12N9/04 ,  C12N9/18 ,  C12N9/86 ,  G06G7/58 ,  G06F19/16 ,  G06F19/18 ,  G06F17/50

Abstract: The invention provides computational methods for engineering, selecting, and/or identifying proteins with a desired activity. Further provided are automated computational design and screening methods to engineer proteins with desired functional activities including, but not limited to ligand binding, catalytic activity, substrate specificity, regioselectivity and/or stereoselectivity.

公开(公告)号：US08340951B2

公开(公告)日：2012-12-25

申请号：US12334360

申请日：2008-12-12

Applicant: David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

Inventor： David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

IPC: G06G7/58 ,  C12N9/14 ,  C07K14/00 ,  C07K17/00

CPC classification number: C12N9/88 ,  G06F19/24

Abstract: Disclosed herein are techniques for computationally designing enzymes. These techniques can be used to design variations of naturally occurring enzymes, as well as new enzymes having no natural counterparts. The techniques are based on first identifying functional reactive sites required to promote the desired reaction. Then, hashing algorithms are used to identify potential protein backbone structures (i.e., scaffolds) capable of supporting the required functional sites. These techniques were used to design 32 different protein sequences that exhibited aldol reaction catalytic function, 31 of which are defined in the Sequence Listing. Details of these 31 different synthetic aldolases are provided, including descriptions of how such synthetic aldolases can be differentiated from naturally occurring aldolases.

Abstract translation: 本文公开了用于计算设计酶的技术。 这些技术可用于设计天然存在的酶的变体，以及不具有天然对应物的新酶。 这些技术基于首先鉴定促进所需反应所需的功能性反应位点。 然后，使用散列算法来鉴定能够支持所需功能位点的潜在的蛋白质主链结构（即支架）。 这些技术用于设计出显示醛醇反应催化功能的32种不同的蛋白质序列，其中31种在序列表中定义。 提供了这31种不同合成醛缩酶的细节，包括如何将这些合成醛缩酶与天然存在的醛缩酶相区分。

公开(公告)号：US20160063177A1

公开(公告)日：2016-03-03

申请号：US14776532

申请日：2014-03-14

Applicant: Alexandre ZANGHELLINI ,  Andrew Yih-En ,  Eric Anthony ALTHOFF ,  Daniela GRABS ,  Mihai Luchian AZOITEI

Inventor： Alexandre ZANGHELLINI ,  Yih-En Andrew BAN ,  Eric Anthony ALTHOFF ,  Daniela GRABS ,  Mihai Luchian AZOITEI

IPC: G06F19/16 ,  G06F17/50 ,  G06F19/18

CPC classification number: G06F19/16 ,  G06F17/50 ,  G06F19/18

Abstract: The invention provides computational methods for engineering, selecting, and/or identifying proteins with a desired activity. Further provided are automated computational design and screening methods to engineer proteins with desired functional activities including, but not limited to ligand binding, catalytic activity, substrate specificity, regioselectivity and/or stereoselectivity.

Abstract translation: 本发明提供了用于工程化，选择和/或鉴定具有所需活性的蛋白质的计算方法。 进一步提供了自动化计算设计和筛选方法来设计具有所需功能活性的蛋白质，包括但不限于配体结合，催化活性，底物特异性，区域选择性和/或立体选择性。

公开(公告)号：US09243238B2

公开(公告)日：2016-01-26

申请号：US13308699

申请日：2011-12-01

Applicant: David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

Inventor： David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

IPC: C12N9/88 ,  G06F19/26 ,  G06F19/24

CPC classification number: C12N9/88 ,  G06F19/24

Abstract: Disclosed herein are techniques for computationally designing enzymes. These techniques can be used to design variations of naturally occurring enzymes, as well as new enzymes having no natural counterparts. The techniques are based on first identifying functional reactive sites required to promote the desired reaction. Then, hashing algorithms are used to identify potential protein backbone structures (i.e., scaffolds) capable of supporting the required functional sites. These techniques were used to design 32 different protein sequences that exhibited aldol reaction catalytic function, 31 of which are defined in the Sequence Listing. Details of these 31 different synthetic aldolases are provided, including descriptions of how such synthetic aldolases can be differentiated from naturally occurring aldolases.

Abstract translation: 本文公开了用于计算设计酶的技术。 这些技术可用于设计天然存在的酶的变体，以及不具有天然对应物的新酶。 这些技术基于首先鉴定促进所需反应所需的功能性反应位点。 然后，使用散列算法来鉴定能够支持所需功能位点的潜在的蛋白质主链结构（即支架）。 这些技术用于设计出显示醛醇反应催化功能的32种不同的蛋白质序列，其中31种在序列表中定义。 提供了这31种不同合成醛缩酶的细节，包括如何将这些合成醛缩酶与天然存在的醛缩酶相区分。

公开(公告)号：US20120142077A1

公开(公告)日：2012-06-07

申请号：US13308699

申请日：2011-12-01

Applicant: David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

Inventor： David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Röthlisberger ,  Eric Althoff

IPC: C12N9/88 ,  C12N9/00

CPC classification number: C12N9/88 ,  G06F19/24

Abstract: Disclosed herein are techniques for computationally designing enzymes. These techniques can be used to design variations of naturally occurring enzymes, as well as new enzymes having no natural counterparts. The techniques are based on first identifying functional reactive sites required to promote the desired reaction. Then, hashing algorithms are used to identify potential protein backbone structures (i.e., scaffolds) capable of supporting the required functional sites. These techniques were used to design 32 different protein sequences that exhibited aldol reaction catalytic function, 31 of which are defined in the Sequence Listing. Details of these 31 different synthetic aldolases are provided, including descriptions of how such synthetic aldolases can be differentiated from naturally occurring aldolases.

Abstract translation: 本文公开了用于计算设计酶的技术。 这些技术可用于设计天然存在的酶的变体，以及不具有天然对应物的新酶。 这些技术基于首先鉴定促进所需反应所需的功能性反应位点。 然后，使用散列算法来鉴定能够支持所需功能位点的潜在的蛋白质主链结构（即支架）。 这些技术用于设计出显示醛醇反应催化功能的32种不同的蛋白质序列，其中31种在序列表中定义。 提供了这31种不同合成醛缩酶的细节，包括如何将这些合成醛缩酶与天然存在的醛缩酶相区分。

公开(公告)号：US20090191607A1

公开(公告)日：2009-07-30

申请号：US12334360

申请日：2008-12-12

Applicant: David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Rothlisberger ,  Eric Althoff

Inventor： David Baker ,  Alexandre Zanghellini ,  Lin Jiang ,  Andrew Wollacott ,  Daniela Grabs-Rothlisberger ,  Eric Althoff

IPC: C12N9/14

CPC classification number: C12N9/88 ,  G06F19/24

Abstract: Disclosed herein are techniques for computationally designing enzymes. These techniques can be used to design variations of naturally occurring enzymes, as well as new enzymes having no natural counterparts. The techniques are based on first identifying functional reactive sites required to promote the desired reaction. Then, hashing algorithms are used to identify potential protein backbone structures (i.e., scaffolds) capable of supporting the required functional sites. These techniques were used to design 32 different protein sequences that exhibited aldol reaction catalytic function, 31 of which are defined in the Sequence Listing. Details of these 31 different synthetic aldolases are provided, including descriptions of how such synthetic aldolases can be differentiated from naturally occurring aldolases.

Abstract translation: 本文公开了用于计算设计酶的技术。 这些技术可用于设计天然存在的酶的变体，以及不具有天然对应物的新酶。 这些技术基于首先鉴定促进所需反应所需的功能性反应位点。 然后，使用散列算法来鉴定能够支持所需功能位点的潜在的蛋白质主链结构（即支架）。 这些技术用于设计出显示醛醇反应催化功能的32种不同的蛋白质序列，其中31种在序列表中定义。 提供了这31种不同合成醛缩酶的细节，包括如何将这些合成醛缩酶与天然存在的醛缩酶相区分。