ZYMEWORKS INC.

Patent Trials and Appeals Board

Jan 26, 2021

2020002595 (P.T.A.B. Jan. 26, 2021)

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.
15/221,379 07/27/2016 Paula I. LARIO 069480-5001-US01 2576
43850 7590 01/26/2021
Morgan, Lewis & Bockius LLP (SF)
One Market, Spear Street Tower, Suite 2800
San Francisco, CA 94105
EXAMINER
NEGIN, RUSSELL SCOTT
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
01/26/2021 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):
donald.mixon@morganlewis.com
sfipdocketing@morganlewis.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte PAULA I. LARIO, JOHANNES MULLEGGER, SURJIT B.
DIXIT, TOMAS RODINGER, and POWELL PATRICK CHENG TAN
Appeal 2020-002595
Application 15/221,379
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and LILAN REN,
Administrative Patent Judges.
REN, Administrative Patent Judge.
DECISION ON APPEAL
STATEMENT OF THE CASE
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1, 5, 10, 15, 38, 40, and 41. See Final
Act. 2, 5. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 We use the word Appellant to refer to “applicant” as defined in 37 C.F.R.
§ 1.42. Appellant identifies the real party in interest as “Zymeworks Inc.”
Appeal Br. 3.
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Application 15/221,379

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CLAIMED SUBJECT MATTER
The claims are directed to “methods of deducing networks of residues
that exhibit related movements within a protein or the network of component
structural units within a biopolymer.” Spec. ¶ 4. Claim 1, reproduced below,
is illustrative of the claimed subject matter:
1. A method of engineering a variant of a polypeptide,
wherein the polypeptide comprises a plurality of residues, the
method comprising:
a) performing a molecular dynamics or Monte Carlo
simulation to calculate a trajectory for a plurality of residue
metrics using a three-dimensional atomic model of the
polypeptide, wherein the plurality of residue metrics comprises a
plane angle for a residue, or a backbone dihedral angle ϕ and ψ
for a residue, or a distance vector r pointing from ʗα to a terminal
atom of a residue for each individual residue in the plurality of
residues;
b) determining at least one residue conformation for each
corresponding residue in the plurality of residues, wherein the at
least one residue conformation of a corresponding residue in the
plurality of residues is obtained by clustering first conformation
information for the corresponding residue in the trajectory,
wherein the first conformation information comprises a subset of
the plurality of residue metrics or the plurality of residue metrics
for the corresponding residue;
c) determining a conformational frequency of each of the
at least one residue conformation of each residue in the plurality
of residues;
d) determining a variance in the residue conformation of
each of the at least one residue conformation of each residue in
the plurality of residues;
e) assigning a mobility index to each respective residue in
the plurality of residues based on the corresponding
conformational frequency and the variance of each residue
conformation in the at least one residue conformation of the
respective residue; and
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f) engineering the variant of the polypeptide, wherein the
variant of the polypeptide comprises the sequence of the
polypeptide in which a first residue of the polypeptide has been
substituted in the variant of the polypeptide for a different residue
at least partly on the basis of the mobility index for the residue.
Claims Appendix (Appeal Br. 26).

REFERENCES
The prior art references relied upon by the Examiner are:
Name Reference Date
Wang US 2001/0051855 A1 Dec. 13, 2001
Prakash US 2005/0119837 A1 June 2, 2005
Robert J. Petrella & Martin Karplus, The Energetics of Off-rotamer Protein
Sidechain Conformations, 312 J. Mol. Biol. 1161–1175 2001.

REJECTIONS
Claims Rejected 35 U.S.C. § Reference(s)/Basis
1, 5, 10, 15, 38, 40, 41 101 Eligibility
1, 5, 10, 15, 38, 40, 41 103 Petrella, Prakash, Wang

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OPINION
Rejection under Section 101
Legal Framework
In determining whether a claim falls within a category excluded from
eligible subject matter, our inquiry focuses on the Supreme Court’s two-step
framework described in Mayo and Alice. Alice Corp. v. CLS Bank Int’l, 573
U.S. 208, 217–18 (2014) (citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75–77 (2012)).
In accordance with that framework, we first determine what concept
the claim is “directed to.” See Alice, 573 U.S. at 219. Concepts determined
to be abstract ideas, and thus patent ineligible, include mental processes
(Gottschalk v. Benson, 409 U.S. 63, 67 (1972)) and mathematical formulas
(Parker v. Flook, 437 U.S. 584, 594–95 (1978)). Concepts determined to be
patent eligible include physical and chemical processes, such as “molding
rubber products” (Diamond v. Diehr, 450 U.S. 175, 191 (1981)); “tanning,
dyeing, making water-proof cloth, vulcanizing India rubber, smelting ores”
(id. at 182 n.7 (quoting Corning v. Burden, 56 U.S. 252, 267–68 (1853)));
and manufacturing flour (Benson, 409 U.S. at 69 (citing Cochrane v.
Deener, 94 U.S. 780, 785 (1876))).
However, not every claim that recites a mathematical formula is
patent ineligible. In Diamond v. Diehr, 450 U.S. 175, 191 (1981), the claim
at issue recited a mathematical formula, but the Supreme Court held that “[a]
claim drawn to subject matter otherwise statutory does not become
nonstatutory simply because it uses a mathematical formula.” Diehr, 450
U.S. at 176; see also id. at 191 (“We view respondents’ claims as nothing
more than a process for molding rubber products and not as an attempt to
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patent a mathematical formula.”). The Supreme Court also indicated that a
claim “seeking patent protection for that formula in the abstract . . . is not
accorded the protection of our patent laws . . . and this principle cannot be
circumvented by attempting to limit the use of the formula to a particular
technological environment.” Id. (citing Flook and Benson); see also, e.g., id.
at 187 (“It is now commonplace that an application of a law of nature or
mathematical formula to a known structure or process may well be deserving
of patent protection.”).
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, where “we must examine the
elements of the claim to determine whether it contains an ‘inventive
concept’ sufficient to ‘transform’ the claimed abstract idea into a patent-
eligible application.” Alice, 573 U.S. at 221 (quotation marks omitted). “A
claim that recites an abstract idea must include ‘additional features’ to
ensure ‘that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea].’” Id. (quoting Mayo, 566 U.S. at 77).
In January 2019, the USPTO published revised guidance on the
application of § 101. 2019 Revised Patent Subject Matter Eligibility
Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019) (the “2019 Revised Guidance”).2
Under the 2019 Revised Guidance, we first look to whether the claim
recites:

2 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the 2019 Revised Guidance.
USPTO, October 2019 Update: Subject Matter Eligibility (the “October
2019 Update”) (available at https://www.uspto.gov/sites/default/files/
documents/peg_oct_2019_update.pdf).
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(1) any judicial exceptions, including certain groupings of abstract
ideas (i.e., mathematical concepts, certain methods of organizing
human activity such as a fundamental economic practice, or mental
processes) (“Step 2A, Prong One”); and
(2) additional elements that integrate the judicial exception into a
practical application (see MPEP § 2106.05(a)–(c), (e)–(h) (9th ed.
2018)) (“Step 2A, Prong Two”).3
2019 Revised Guidance, 84 Fed. Reg. at 52–55. Only if a claim (1) recites a
judicial exception and (2) does not integrate that exception into a practical
application, do we then look, under Step 2B, to whether the claim:
(3) adds a specific limitation beyond the judicial exception that is not
“well-understood, routine, conventional” in the field (see MPEP
§ 2106.05(d)); or
(4) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of
generality, to the judicial exception.
See 2019 Revised Guidance, 84 Fed. Reg. at 52, 55–56.
Judicial Exception (Step 2A, Prong One)
In rejecting claim 1, the Examiner finds that the “claims are directed
to the judicial exceptions of performing molecular dynamics simulations,
determining structural unit conformation information, determining
conformational frequency and variance, and determining a mobility index.”
Final Act. 2–3. The Examiner reasons, without analysis, that “[t]he claims
do not recite practical applications of the judicial exceptions because the

3 We perform this evaluation by (a) identifying whether there are any
additional elements recited in the claim beyond the judicial exception, and
(b) evaluating those additional elements individually and in combination to
determine whether the claim as a whole integrates the exception into a
practical application. See 2019 Revised Guidance - Section III(A)(2),
84 Fed. Reg. at 54–55.
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algorithmic fact pattern of the claims is not analogous to an algorithmic fact
pattern of claims in precedential Court decisions which were found to be
patent eligible.” Id. at 3. The Examiner also finds that the claims “do not
include additional elements that are sufficient to amount to significantly
more than the judicial exception” because “conducting X-ray and NMR
measurements on proteins in corresponding molecular dynamics simulations
is routine and conventional.” Id. (citing Karplus et al., 347 Nature 631–639
(1990)).
We do not sustain the rejection based on the record before us because
the rejection does not thoroughly follow the 2019 Revised Guidance in
analyzing patent eligibility. For example, the analysis does not clearly state
that the claims are directed to an abstract idea. See Final Act. 3; See Alice,
573 U.S. at 219. The analysis does not explain why the identified concepts
recited in the claims are determined to be abstract ideas, such as mental
processes (Gottschalk v. Benson, 409 U.S. 63, 67 (1972)) or mathematical
formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)). See 2019 Revised
Guidance, 84 Fed. Reg. at 52 (explaining that mathematical concepts and
mental processes are among the groupings of subject matter which are
abstract ideas). The analysis does not specifically identify the additional
elements in the claims and explain why those elements do not integrate the
judicial exceptions into a practical application. See 2019 Revised Guidance,
84 Fed. Reg. at 54–55. The analysis also does not “examine the elements of
the claim to determine whether it contains an ‘inventive concept’ sufficient
to ‘transform’ the claimed abstract idea into a patent-eligible application.”
Alice, 573 U.S. at 221 (citations omitted); see also 2019 Revised Guidance,
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84 Fed. Reg. at 56. The rejection under section 101 is accordingly not
sustained.
Rejection under Section 103
“[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting a prima facie case of unpatentability.” In
re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). To establish a prima facie
case of obviousness, the Examiner must show that each and every limitation
of the claim is described or suggested by the prior art or would have been
obvious based on the knowledge of those of ordinary skill in the art. In re
Fine, 837 F.2d 1071, 1074 (Fed. Cir. 1988).
In this case, the Examiner acknowledges that Petrella “does not teach
clustering” (Final Act. 6) – presumably referring to the limitation of “the at
least one residue conformation of a corresponding residue in the plurality of
residues is obtained by clustering first conformation information for the
corresponding residue in the trajectory.” The Examiner finds, however, that
Prakash “teach[es] clustering in conjunction with the simulation.” Final Act.
7.
Appellant argues that the record does not sufficiently support a
showing that the recited “at least one residue conformation of a
corresponding residue in the plurality of residues is obtained by clustering
first conformation information for the corresponding residue in the
trajectory” is taught or suggested by Prakash. Appeal Br. 22. The Examiner
does not address the claim limitation other than stating that Prakash “is
relied upon for clustering; in this obviousness prior art rejection the teaching
clustering in general is adequate to at least suggest the clustering limitation
of the claims.” Ans. 6. Because the record before us lacks evidentiary
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support for the teaching or suggestion of the limitation at issue, we do not
sustain the obviousness rejection.4

CONCLUSION
The Examiner’s rejections are reversed.

DECISION SUMMARY
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 5, 10, 15,
38, 40, 41
101 Eligibility 1, 5, 10, 15,
38, 40, 41
1, 5, 10, 15,
38, 40, 41
103 Petrella, Prakash,
Wang
1, 5, 10, 15,
38, 40, 41
Overall
Outcome
1, 5, 10, 15,
38, 40, 41

REVERSED

4 Given our reversal of the obviousness rejection based on the claim
limitation at issue, we decline to address other arguments raised by
Appellant as they are unnecessary for the disposition of this case.