Ex Parte Ohrn et al

Patent Trial and Appeal Board

Sep 22, 2017

14386711 (P.T.A.B. Sep. 22, 2017)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O.Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/386,711 09/19/2014 Anders Ohrn 069480-5009-US 4640
43850 7590 09/26/2017
MORGAN, LEWIS & BOCKIUS LLP (SF)
One Market, Spear Street Tower, Suite 2800
San Francisco, CA 94105
EXAMINER
OCHOA, JUAN CARLOS
ART UNIT PAPER NUMBER
2123
NOTIFICATION DATE DELIVERY MODE
09/26/2017 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
sfipdocketing @ morganlewis.com
donald.mixon@morganlewis.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ANDERS OHRN and SCOTT PAUL MACDONALD
Appeal 2017-005630
Application 14/3 86,7111
Technology Center 2100
Before LINZY T. McCARTNEY, NATHAN A. ENGELS, and
JAMES W. DEJMEK, Administrative Patent Judges.
DEJMEK, Administrative Patent Judge.
DECISION ON APPEAL
Appellants appeal under 35 U.S.C. § 134(a) from a Final Rejection of
claims 1—48. We have jurisdiction over the pending claims under 35 U.S.C.
§ 6(b).
We affirm.
1 Appellants identify Perceptive Credit Opportunities Fund, L.P., Assignee
of record, and Zymeworks, Inc. as the real parties in interest. App. Br. 3.
Appeal 2017-005630
Application 14/386,711
STATEMENT OF THE CASE
Introduction
Appellants’ disclosed and claimed invention is directed to systems
and methods for minimizing a cost function. Spec. 17. According to the
Specification, complex molecules typically have many discrete particles and
adopt unique, complex three-dimensional conformations, which makes
visualization of the molecules’ physical properties challenging. Spec. Tflf 3,
4. Thus, Appellants’ claimed invention seeks to minimize a so-called cost
function to reduce the loss of structural fidelity while compressing three-
dimensional data coordinates into a two-dimensional graph. Spec. Tflf 5, 7, 8.
The Specification describes the cost function as “containing the error in the
set of two-dimensional coordinates (ci, ... , Cn) ... [wherein each] Ci in (ci,
... , cn) corresponds to a three-dimensional coordinate X, in [x/, ••• , x^}.”
Spec. 17. Further, the Specification discloses using a dimension reduction
scheme (e.g., linear principal component analysis) to devise an initial set of
two-dimensional coordinates from a set of three-dimensional coordinates.
Spec. 17.
Claim 1 is representative of the subject matter on appeal and is
reproduced below:
1. A computer-implemented method for automating a
macromolecular structural study associated with drug discovery
or diagnostic development, the method performed on a computer
system having at least one processor and memory storing at least
one program for execution by the at least one processor to
perform the method, comprising:
(A) obtaining a set of A three-dimensional coordinates (xi,
. . . , xat} , stored in the memory, for a molecule that comprises a
set of (pi,. . ., pv} particles, each particle Pi in the set of particles
representing a different plurality of covalently bound atoms in
the molecule, wherein each respective Xi in (xi,. . . , x^}
2
Appeal 2017-005630
Application 14/386,711
corresponds to a pi in {pi, ... , pjv} and represents the position of
pi in three-dimensional space;
(B) using a minimization function module stored in the
memory to automatically minimize a cost function:
i and j are integers greater than zero,
bij is a distance between a pair of three-dimensional
coordinates x, and x7 in {xi, . . . , x^},
E{c\, C2, , cn) is an error in the set of two-dimensional
coordinates (ci, ... , Cat), wherein each two-dimensional
coordinate ci in (ci, ... , Cn) uniquely corresponds to a
three-dimensional coordinates xi in {xl, . . . , x^} so that each
respective pi in {pi, ... , pAr} is represented by a
three-dimensional coordinate xi in {xi, ... , x^J and a
corresponding two-dimensional coordinate ci in (ci, . . . , Cat),
D(d, q) is a distance between the two-dimensional
coordinates c, and cy in (ci,. . ., cat), and
Wij is a weight for the two-dimensional pair (p„ p7) in a
matrix of weights, wherein the matrix of weights has a weight for
each two-dimensional pair (p„ p7) in (pi, . . . , pA,
wherein the minimizing alters the values of coordinates of the set
of two-dimensional coordinates (ci, ... , Cn) using a refinement
algorithm until an exit condition is achieved;
(C) automatically obtaining a first set of physical properties Sm,
each physical property sq in Sm representing a physical property shared
by a pair of particles (pi, pj) in {pi,..., pAr};
(D) automatically plotting (ci,. . ., Cat), after the exit condition is
achieved, as a plurality of nodes of a two-dimensional graph; and
(E) automatically plotting a plurality of edges for the
two-dimensional graph, wherein each respective edge in the plurality
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