Mark R Hansen

US Patent:

6727058, Apr 27, 2004

Filed:

Mar 12, 2001

Appl. No.:

09/803863

Inventors:

Frederic Bushman - Encinitas CA
Mark Hansen - San Diego CA

Assignee:

The Salk Institute for Biological Studies - La Jolla CA

International Classification:

C12Q 170

US Classification:

435 5, 435 6, 435 691, 435239, 435183

Abstract:

The present invention provides packaging cell lines and recombinant lentiviral or retroviral particles produced therefrom, particularly pseudotyped retroviral particles. The packaging cell lines of the invention are produced by inducibly expressing an envelope protein by methods described herein. Also described is a screening assay for compounds that affect integration of viral nucleic acid into target (e. g. , host) nucleic acid. Such compounds are identified based on their effect on viral integrase.

US Patent:

6792355, Sep 14, 2004

Filed:

Dec 21, 2001

Appl. No.:

10/032395

Inventors:

Mark R. Hansen - San Diego CA
Richard Kho - San Diego CA
Hugo O. Villar - La Jolla CA

Assignee:

Triad Therapeutics, Inc. - San Diego CA

International Classification:

G06F 1700

US Classification:

702 19, 702 20

Abstract:

The invention provides a method for separating two or more subsets of polypeptides within a set of polypeptides. The method includes the steps of: (a) determining a sequence comparison signature for each amino acid sequence in a set of amino acid sequences, wherein the sequence comparison signature includes pairwise comparison scores for the amino acid sequence compared to each of the other amino acid sequences in the set; (b) constructing a distance arrangement including the sequence comparison signatures related according to the distance between each of the sequence comparison signatures; and (c) identifying a first and second cluster of sequence comparison signatures in the distance arrangement, wherein the first cluster includes sequence comparison signatures for polypeptides having a similar protein fold or biological function, the protein fold or function being different compared to a protein fold or function of polypeptides having sequence comparison signatures in the second cluster.

US Patent:

20020133296, Sep 19, 2002

Filed:

Dec 22, 2000

Appl. No.:

09/747174

Inventors:

Daniel Sem - San Diego CA, US
Mark Hansen - San Diego CA, US

International Classification:

G06F019/00
G01N033/48
G01N033/50

US Classification:

702/019000, 530/388100

Abstract:

The invention provides a method for identifying a pharmacocluster. The method includes the steps of (a) determining bound conformations of a ligand bound to different polypeptides, and (b) clustering two or more bound conformations of the ligand having substantially the same bound conformation, thereby identifying a pharmacocluster. The invention also provides a method for identifying a member of a pharmacocluster. The invention also provides a method for identifying a polypeptide pharmacofamily. The method includes the steps of (a) determining bound conformations of a ligand bound to different polypeptides of a polypeptide family, and (b) identifying two or more bound conformations of the ligand having substantially different bound conformations, thereby identifying at least two polypeptide pharmacofamilies exhibiting binding specificity for the two or more substantially different bound conformations of the ligand.

US Patent:

20030162219, Aug 28, 2003

Filed:

Dec 28, 2001

Appl. No.:

10/040895

Inventors:

Daniel Sem - San Diego CA, US
Brian Baker - Poway CA, US
Mark Hansen - San Diego CA, US

International Classification:

G01N033/53
G06F019/00
G01N033/48
G01N033/50

US Classification:

435/007100, 702/019000

Abstract:

The invention provides a method for identifying a polypeptide that binds a ligand. The method includes the steps of (a) comparing a sequence of a polypeptide to a sequence model for polypeptides that bind a ligand, wherein the sequence model comprises representations of amino acids consisting of a subset of amino acids, the subset of amino acids having one or more atom within a selected distance from a bound ligand in the polypeptides that bind the ligand; and (b) determining a relationship between the sequence and the sequence model, wherein a correspondence between the sequence and the sequence model identifies the polypeptide as a polypeptide that binds the ligand.

US Patent:

20030228621, Dec 11, 2003

Filed:

Jul 2, 2002

Appl. No.:

10/189327

Inventors:

Yong Qin - Poway CA, US
Lin Yu - San Diego CA, US
Mark Hansen - San Diego CA, US
Eduard Sergienko - San Diego CA, US
Bonnie Bertolaet - San Diego CA, US
Daniel Sem - New Berlin WI, US

International Classification:

G01N033/53
C12Q001/26

US Classification:

435/007100, 435/025000

Abstract:

The present invention provides compositions containing a common ligand linked to a detectable moiety and provides methods for the preparation of such compositions. The present invention also provides methods for screening candidate ligands for binding to a NAD binding receptor, which include contacting a receptor with a candidate ligand and a composition of the invention followed by evaluation of receptor binding. The screening method of the present invention has broad applicability and can be used to screen large numbers of a wide variety of ligands. The present invention further provides methods for detecting the binding activity of a putative receptor, which include combining the putative receptor with a composition of the invention and evaluating the level of detectable moiety. The invention also provides kits useful for detection of receptors having NAD binding activity and for screening of candidate ligands that bind to a NAD binding receptor.

US Patent:

20030236630, Dec 25, 2003

Filed:

Jul 26, 2002

Appl. No.:

10/206786

Inventors:

Daniel Sem - San Diego CA, US
Mark Hansen - San Diego CA, US

Assignee:

Triad Therapeutics, Inc.

International Classification:

G06F019/00
G01N033/48
G01N033/50

US Classification:

702/019000

Abstract:

The invention provides a method for identifying a pharmacocluster. The method includes the steps of (a) determining bound conformations of a ligand bound to different polypeptides, and (b) clustering two or more bound conformations of the ligand having substantially the same bound conformation, thereby identifying a pharmacocluster. The invention also provides a method for identifying a member of a pharmacocluster. The invention also provides a method for identifying a polypeptide pharmacofamily. The method includes the steps of (a) determining bound conformations of a ligand bound to different polypeptides of a polypeptide family, and (b) identifying two or more bound conformations of the ligand having substantially different bound conformations, thereby identifying at least two polypeptide pharmacofamilies exhibiting binding specificity for the two or more substantially different bound conformations of the ligand.

US Patent:

20040009526, Jan 15, 2004

Filed:

Feb 21, 2002

Appl. No.:

10/081989

Inventors:

Lin Yu - San Diego CA, US
Qing Dong - San Diego CA, US
Fabrice Pierre - La Jolla CA, US
Edcon Chang - San Diego CA, US
Hengyuan Lang - San Diego CA, US
Yong Qin - Poway CA, US
Yunfeng Fang - San Diego CA, US
Mark Hansen - San Diego CA, US
Maurizio Pellecchia - San Diego CA, US

International Classification:

G01N033/53
C07D413/02
C07K005/06
G01N033/543

US Classification:

435/007100, 530/331000, 548/183000, 436/518000

Abstract:

The present invention provides common ligand mimics that act as common ligands for a receptor family. The present invention also provides bi-ligands containing these common ligand mimics. Bi-ligands of the invention provide enhanced affinity and/or selectivity of ligand binding to a receptor or receptor family through the synergistic action of the common ligand mimic and specificity ligand which compose the bi-ligand. The present invention also provides combinatorial libraries containing the common ligand mimics and bi-ligands of the invention. Further, the present invention provides methods for manufacturing the common ligand mimics and bi-ligands of the invention and methods for assaying the combinatorial libraries of the invention.

US Patent:

20040009527, Jan 15, 2004

Filed:

Mar 15, 2002

Appl. No.:

10/099136

Inventors:

Qing Dong - San Diego CA, US
Fabrice Pierre - La Jolla CA, US
Hengyuan Lang - San Diego CA, US
Lin Yu - San Diego CA, US
Mark Hansen - San Diego CA, US
Daniel Sem - San Diego CA, US
Maurizio Pellecchia - San Diego CA, US

International Classification:

G01N033/53
C07D417/02
C07D277/38
G01N033/543

US Classification:

435/007100, 548/184000, 546/269700, 436/518000

Abstract:

The present invention provides common ligand mimics that act as common ligands for a receptor family. The present invention also provides bi-ligands containing these common ligand mimics. Bi-ligands of the invention provide enhanced affinity and/or selectivity of ligand binding to a receptor or receptor family through the synergistic action of the common ligand mimic and specificity ligand that compose the bi-ligand. The present invention also provides combinatorial libraries containing the common ligand mimics and bi-ligands of the invention. Further, the present invention provides methods for manufacturing the common ligand mimics and bi-ligands of the invention and methods for assaying the combinatorial libraries of the invention.