Donald Scott Baskerville

US Patent:

6429301, Aug 6, 2002

Filed:

Oct 31, 2000

Appl. No.:

09/702543

Inventors:

Donald Scott Baskerville - Brighton MA
David P. Bartel - Brookline MA

Assignee:

Whitehead Institute for Biomedical Research - Cambridge MA

International Classification:

C07H 2102

US Classification:

536 231, 536 241

Abstract:

Engineered mRNA useful in producing libraries of engineered mRNAs, polypeptide-engineered mRNA conjugates and diverse encoded polypeptide libraries, as well as novel ribozymes that join an mRNA to the translation product of the mRNA and methods of identifying members of diverse encoded polypeptide libraries which exhibit a desired activity. Also described are polypeptide-nucleic acid tag conjugates, methods of producing the conjugates and uses therefor.

US Patent:

6716973, Apr 6, 2004

Filed:

Jun 20, 2002

Appl. No.:

10/177257

Inventors:

Donald Scott Baskerville - Brighton MA
David P. Bartel - Brookline MA

Assignee:

Whitehead Institute for Biomedical Research - Cambridge MA

International Classification:

C07H 2102

US Classification:

536 231, 536 241

Abstract:

Engineered mRNA useful in producing libraries of engineered mRNAs, polypeptide-engineered mRNA conjugates and diverse encoded polypeptide libraries, as well as novel ribozymes that join an mRNA to the translation product of the mRNA and methods of identifying members of diverse encoded polypeptide libraries which exhibit a desired activity. Also described are polypeptide-nucleic acid tag conjugates, methods of producing the conjugates and uses therefor.

US Patent:

61435031, Nov 7, 2000

Filed:

Apr 14, 1999

Appl. No.:

9/291837

Inventors:

Donald Scott Baskerville - Newton MA
David P. Bartel - Brookline MA

Assignee:

Whitehead Institute for Biomedical Research - Cambridge MA

International Classification:

C12Q 168
C12P 1934
C07H 2104

US Classification:

435 6

Abstract:

Engineered mRNA useful in producing libraries of engineered mRNAs, polypeptide-engineered mRNA conjugates and diverse encoded polypeptide libraries, as well as novel ribozymes that join an mRNA to the translation product of the mRNA and methods of identifying members of diverse encoded polypeptide libraries which exhibit a desired activity. Also described are polypeptide-nucleic acid tag conjugates, methods of producing the conjugates and uses therefor.

US Patent:

20220238179, Jul 28, 2022

Filed:

Apr 12, 2022

Appl. No.:

17/719321

Inventors:

- Redwood City CA, US
Donald Scott Baskerville - Burlingame CA, US
Xiyun Zhang - Fremont CA, US

International Classification:

G16B 15/00
G16B 40/00
G16B 5/00
G16C 10/00
G16B 35/20
G16B 15/30
C12N 15/10
G16B 15/20

Abstract:

Disclosed are methods for building a sequence activity model with reference to structural data, which model can be used to guide directed evolution of proteins having beneficial properties. Some embodiments use genetic algorithms and structural data to filter out uninformative data. Some embodiments use a support vector machine to train the sequence activity model. The filtering and training methods can generate a sequence activity model having higher predictive power than conventional modeling methods. Systems and computer program products implementing the methods are also provided.

US Patent:

20230048421, Feb 16, 2023

Filed:

Nov 2, 2022

Appl. No.:

17/979711

Inventors:

- Redwood City CA, US
Russell Javiniar Sarmiento - Redwood City CA, US
Donald Scott Baskerville - Burlingame CA, US
Gjalt W. Huisman - Redwood City CA, US

Assignee:

Codexis, Inc. - Redwood City CA

International Classification:

C12N 15/10
G16B 35/00
G16B 35/20
G16C 20/60

Abstract:

Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.

US Patent:

20210309977, Oct 7, 2021

Filed:

Jun 11, 2021

Appl. No.:

17/345404

Inventors:

- Redwood City CA, US
Vesna Mitchell - Santa Clara CA, US
Jovana Nazor - Milpitas CA, US
Donald S. Baskerville - Louisville CO, US
Nikki Dellas - San Carlos CA, US
David Elgart - San Mateo CA, US
Jonathan Vroom - South San Francisco CA, US
Sandy M. Gomes - Redwood City CA, US
Nandhitha Subramanian - Cambridge, GB
Ericka Bermudez - Aptos CA, US

International Classification:

C12N 9/12

Abstract:

The present invention provides engineered DNA polymerase polypeptides and compositions thereof, as well as polynucleotides encoding the engineered DNA polymerase polypeptides. The invention also provides methods for use of the compositions comprising the engineered DNA polymerase polypeptides for diagnostic and other purposes.

US Patent:

20200277597, Sep 3, 2020

Filed:

May 15, 2020

Appl. No.:

16/875848

Inventors:

- Redwood City CA, US
Russell Javiniar Sarmiento - Redwood City CA, US
Donald Scott Baskerville - Burlingame CA, US
Gjalt W. Huisman - Redwood City CA, US

International Classification:

C12N 15/10
G16C 20/60
G16B 35/00

Abstract:

Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.

US Patent:

20200020415, Jan 16, 2020

Filed:

Jun 6, 2019

Appl. No.:

16/434138

Inventors:

- Redwood City CA, US
Donald Scott Baskerville - Burlingame CA, US
Xiyun Zhang - Fremont CA, US

International Classification:

G16B 5/00
G16B 35/20
C12N 15/10
G16C 10/00
G16B 15/30

Abstract:

Disclosed are methods for building a sequence activity model with reference to structural data, which model can be used to guide directed evolution of proteins having beneficial properties. Some embodiments use genetic algorithms and structural data to filter out uninformative data. Some embodiments use a support vector machine to train the sequence activity model. The filtering and training methods can generate a sequence activity model having higher predictive power than conventional modeling methods. Systems and computer program products implementing the methods are also provided.