ZYMEWORKS INC.

Patent Trials and Appeals Board

Nov 23, 2020

2020002488 (P.T.A.B. Nov. 23, 2020)

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.
14/409,419 12/18/2014 Gregory Lakatos 069480-5010-US 4037
43850 7590 11/23/2020
Morgan, Lewis & Bockius LLP (SF)
One Market, Spear Street Tower, Suite 2800
San Francisco, CA 94105
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
11/23/2020 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 GREGORY LAKATOS and SURJIT BHIMARAO DIXIT1
Appeal 2020-002488
Application 14/409,419
Technology Center 1600
Before DONALD E. ADAMS, ERIC B. GRIMES, and
FRANCISCO C. PRATS, Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method of modeling the effect of a mutation on a polypeptide, which have
been rejected as being ineligible for patenting. We have jurisdiction under
35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Zymeworks, Inc. Appeal
Br. 3. We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42.
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STATEMENT OF THE CASE
The Specification states that
[p]rotein engineering frequently involves investigating the
properties of a known wild-type sequence, making mutations in
a protein of known sequence and structure, and evaluating the
effects of these mutations on properties such as protein fold
stability, or protein binding. An understanding of the
thermodynamically relevant structural configurations of the
wild-type and mutated proteins is beneficial when evaluating
the effects of such mutations.
Spec. ¶ 4. The Specification
describes systems and methods for identifying the
thermodynamically relevant configurations of a polymer or
polymer region. The systems and methods combine
configurational sampling and structural clustering algorithms in
novel ways to identify sets of polymer configurations that are
mutually distinct, and have free energies close to the
thermodynamic ground state.
Id. ¶ 15.
Claims 1, 4, 5, 7, 9–15, 18, 19, 22, 23, 27–30, 36, 38, 40, 41, 44, and
45 are on appeal. Claim 1, reproduced below, is illustrative:
1. A method of evaluating an effect that a mutation of a polypeptide
of known sequence and structure has on the polypeptide by
identifying one or more conformations for the polypeptide upon
incorporation of the mutation, wherein the polypeptide comprises a
plurality of atoms, and wherein the polypeptide comprises at least one
contiguous segment of main chain, the method comprising:
at a computer system having one or more processors and
memory storing one or more programs to be executed by the one of
more processors:
(A) obtaining an initial set of three-dimensional coordinates
{x1, ..., xN} for the polypeptide, wherein each respective xi in {x1, ...,
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xN} is a three dimensional coordinate for an atom in the plurality of
atoms in said polypeptide;
(B) identifying, in silico, a residue of the polypeptide, and
replacing the residue with a different residue, thereby defining a
sequence of a mutated polypeptide;
(C) identifying a region of the polypeptide based upon the
identity of the replaced residue of the mutated polypeptide, the region
comprising a plurality of residues;
(D) altering a side-chain rotamer conformation, with respect to
the initial set of three-dimensional coordinates {x1, ..., xN} of each
residue in a subset of residues in the region of the polypeptide, for
each respective subset of residues in the region of the polypeptide in a
plurality of subsets of residues in the region of the polypeptide,
thereby deriving a plurality of mutated polypeptide structures of the
region of the polypeptide,
wherein each respective subset of residues in the plurality of
subsets of residues in the region of the polypeptide is selected from
among all the residues in the region of the polypeptide using a
deterministic, randomized or pseudo-randomized algorithm;
(E) generating a plurality of sets of clusters for each respective
residue in the region of the polypeptide, using the plurality of mutated
polypeptide structures derived in (D), wherein
each respective set of clusters in the plurality of sets of
clusters is for
(i) a side chain or a main chain of a respective residue in
the region of the polypeptide in which each respective cluster in
the respective set of clusters is formed by clustering a
conformation of the side chain or main chain of the respective
residue in each mutated polypeptide structure in the plurality of
mutated polypeptide structures derived in (D) or
(ii) a contiguous segment of the main chain in the at least
one contiguous segment of main chain in the region of the
polypeptide in which each respective cluster in the respective
set of clusters is formed by clustering a structural metric
associated with the main chain of the contiguous segment of the
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main chain in each mutated polypeptide structure in the
plurality of mutated polypeptide structures derived in (D);
(F) grouping respective mutated polypeptide structures in the
plurality of mutated polypeptide structures into a plurality of
subgroups, wherein each mutated polypeptide structure in a subgroup
in the plurality of subgroups falls into the same cluster in a threshold
number of the sets of clusters in the plurality of sets of clusters; and
(G) determining a free energy estimate or configurational
entropy of a plurality of mutated polypeptide structures in each
subgroup in the plurality of subgroups, thereby identifying the effect
that the mutation of the polypeptide has on the polypeptide in the form
of the free energy estimate or the configurational entropy in each
subgroup in the plurality of subgroups.

Claims 44 and 45 are also independent. Claim 44 is directed to a
computer system comprising memory storing at least one program and
instructions for carrying out the steps described in claim 1. Claim 45 is
directed to a computer readable storage medium storing a computational
model comprising instructions for carrying out the steps recited in claim 1.
OPINION
Claims 1, 4, 5, 7, 9–15, 18, 19, 22, 23, 27–30, 36, 38, 40, 41, 44, and
452 stand rejected under 35 U.S.C. § 101 on the basis that “the claimed
invention is directed to non-statutory subject matter.” Ans. 3. The Examiner
finds that the claims recite an abstract idea in the form of mathematical
concepts and/or a mental process. Id. at 4.

2 The statement of the rejection omits claim 36 and includes claim 39. Ans.
3. However, claim 39 has been canceled and the Examiner has indicated that
no claims are allowable. See Amdt. filed May 23, 2018; Final Action 1.
Thus, we understand the rejection to apply to all of the pending claims,
including claim 36.
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More specifically, the Examiner finds that
[s]teps drawn to a mental process recited in the claims include
[(]A) obtaining an initial set of three-dimensional coordinates;
(B) identifying a residue of the polypeptide, and replacing the
residue with a different residue;
(C) identifying a region of the polypeptide;
(D) altering a side-chain rotamer conformation, [t]hereby
deriving a plurality of mutated polypeptide structures of the
region of the polypeptide;
(E) generating a plurality of sets of clusters;
(F) grouping polypeptide structures into a plurality of
subgroups; and
(G) determining a free energy estimate or configurational
entropy.
Id. at 5. The Examiner reasons that “[t]he steps are able to be performed in
the mind, but for the recitation of the computer system. . . . [N]othing in the
claim element precludes the step from practically being performed in the
human mind.” Id.
The Examiner also finds that “[m]athematical concepts recited in the
claims include ‘determining a free energy estimate or configurational
entropy’” because the Specification “indicate[s] that the determination of the
claimed values is a matter of mathematical computation.” Id. at 6.
The Examiner finds that the recited abstract ideas are not integrated
into a practical application because “[t]here are no positive process
limitations recited in the claim for actually using the information produced
by the abstract idea outside of the computer (e.g. a real-world practical
application or solution to a problem)” and “using a processor to perform the
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method steps amounts to no more than mere instructions to apply the
exception using a generic computer component.” Id. at 6–7.
Finally, the Examiner finds that the claimed method “merely requires
generic computer implementation. . . . Therefore, the claims as a whole do
not provide significantly more than a generic computer upon which the
claimed method steps are executed.” Id. at 8.
Appellant argues that “[t]he limitations of claim 1 are not directed to
mere mathematical relationships, mathematical formulas or equations, or
mathematical calculations.” Appeal Br. 13. Appellant also argues that “a
person of skill in the art would understand that the claimed steps . . . cannot,
as a practical matter, be performed in a human mind. Indeed, the entire field
of protein modeling and engineering became possible with the advent of
computing technologies.” Id.
Appellant also argues that “the additional elements [of claim 1] in
combination provide an improvement to a technical field or technical fields,
namely, protein engineering. Indeed, claim 1 embodies a specific,
meaningful way that provides an improvement in the field of rational protein
design and modeling.” Id. at 14. That is, the “claims are focused on a
specific solution to a problem in the rational protein design and modeling
arts—i.e., that conventional methods evaluating an effect that a mutation of
a polypeptide of known sequence and structure has on the polypeptide are
unsatisfactory because of the limitations in the art of rational protein
design.” Id. at 16. Appellant argues that “the specific [claimed] method for
evaluating an effect that a mutation of a polypeptide of known sequence and
structure has on the polypeptide . . . provides the requisite specificity
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required to transform the claim from one claiming only a result, as in
Electric Power Group, to one claiming a way of achieving it, as in McRO.”
Id. at 17.
Principles of Law
A. Section 101
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the U.S. Supreme Court has long interpreted 35 U.S.C. § 101 to
include implicit exceptions: “[l]aws of nature, natural phenomena, and
abstract ideas” are not patentable. E.g., Alice Corp. v. CLS Bank Int’l, 573
U.S. 208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Court’s two-part framework, described in Mayo and Alice.
Id. at 217–18 (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
(“On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4
in petitioners’ application explain the basic concept of hedging, or protecting
against risk.”).
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219–20; Bilski, 561 U.S. at 611);
mathematical formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)); and
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mental processes (Gottschalk v. Benson, 409 U.S. 63, 67 (1972)). 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 (1854))); and manufacturing flour (Benson, 409 U.S. at 69
(citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))).
In Diehr, the claim at issue recited a mathematical formula, but the
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 187; 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 patent a mathematical formula.”). Having said that, the 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. (citation omitted)
(citing Benson and Flook); see, 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 (internal quotation marks
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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. (alterations in original) (quoting Mayo,
566 U.S. at 77). “[M]erely requir[ing] generic computer implementation[]
fail[s] to transform that abstract idea into a patent-eligible invention.” Id.
B. USPTO Section 101 Guidance
In January 2019, the U.S. Patent and Trademark Office (USPTO)
published revised guidance on the application of § 101. See 2019 Revised
Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019)
(“Revised Guidance”).3 “All USPTO personnel are, as a matter of internal
agency management, expected to follow the guidance.” Id. at 51; see also
October 2019 Update at 1.
Under the Revised Guidance and the October 2019 Update, we first
look to whether the claim recites:
(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

3 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the 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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(2) additional elements that integrate the judicial exception into
a practical application (see MPEP §§ 2106.05(a)–(c), (e)–(h)
(9th ed. Rev. 08.2017, Jan. 2018)) (“Step 2A, Prong Two”).4
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.
Revised Guidance, 84 Fed. Reg. at 52–56.
Revised Guidance Step 2A, Prong 1
Following the Revised Guidance, we first consider whether the claims
recite a judicial exception. The Revised Guidance identifies three groupings
of subject matter included in the abstract idea exception, including “[m]ental
processes—concepts performed in the human mind (including an
observation, evaluation, judgment, opinion).” 84 Fed. Reg. at 52.

4 This evaluation is performed 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 Revised Guidance - Section III(A)(2), 84 Fed. Reg.
54–55.
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Claim 1 recites the steps of:
(A) obtaining an initial set of three-dimensional coordinates
{x1, ..., xN} for the polypeptide, wherein each respective xi in {x1, ...,
xN} is a three dimensional coordinate for an atom in the plurality of
atoms in said polypeptide;
(B) identifying, in silico, a residue of the polypeptide, and
replacing the residue with a different residue, thereby defining a
sequence of a mutated polypeptide; [and]
(C) identifying a region of the polypeptide based upon the identity
of the replaced residue of the mutated polypeptide, the region comprising
a plurality of residues.
We agree with the Examiner that these steps encompass abstract ideas
in the category of mental processes. With regard to step (A), the
Specification states that “[i]n some embodiments, the initial structural
coordinates {x1, ..., xN} 46 for the complex molecule of interest are obtained
by x-ray crystallography, nuclear magnetic resonance spectroscopic
techniques, or electron microscopy.” Spec. ¶ 52. However, the claim
language does not require any of these techniques, and the Specification
makes clear that the initial coordinates can also be obtained simply by
accessing a database. See id. ¶ 115 (“The example makes use of an antibody
Fc structure (PDB Accession ID 1E4K), herein referred to as the wild type
structure.”). Observing information existing in a database can practically be
performed in the human mind, and is therefore a mental process.
Likewise, “identifying” an amino acid in a polypeptide and
“replacing” it to “defin[e] a sequence of a mutated polypeptide” (step (B))
can be carried out in the human mind and therefore encompasses a mental
process, notwithstanding the recitation of “in silico.” See Revised Guidance,
84 Fed. Reg. 52 n.14 (“If a claim, under its broadest reasonable
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interpretation, covers performance in the mind but for the recitation of
generic computer components, then it is still in the mental processes
category unless the claim cannot practically be performed in the mind.”).
The same is true of “identifying a region of the polypeptide based upon the
identity of the replaced residue” (step (C)).
However, we do not agree with the Examiner that the remaining steps
of claim 1 can be “performed in the mind, but for the recitation of the
computer system.” Ans. 5. The Examiner has not established that steps (D)
through (G)—altering side chain rotamer conformations and thereby
deriving mutated polypeptide structures, clustering based on side chain or
main chain conformation, grouping the mutated polypeptide structures based
on the clustering, and determining free energy estimates or configurational
entropies—can practically be performed in the human mind.
Nor do we agree with the Examiner that the recited step of
“determining a free energy estimate or configurational entropy of a plurality
of mutated polypeptide structures” (claim 1) recites a mathematical concept.
Ans. 6. While determining a free energy estimate or configurational entropy
undoubtedly involves mathematics, “[a] claim does not recite a mathematical
concept (i.e., the claim limitations do not fall within the mathematical
concept grouping), if it is only based on or involves a mathematical
concept.” October 2019 Update at 3. In addition, the Examiner points to the
Specification’s paragraph 23 and dependent claim 11 as “indicat[ing] that
the determination of the claimed values is a matter of mathematical
computation.” Ans. 6. Both the Specification’s paragraph 23 and dependent
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claim 11, however, address a probability function (P(ΔE)), not free energy or
configurational entropy calculations.
In summary, steps (A), (B), and (C) of claim 1 can practically be
performed in the human mind, and therefore recite an abstract idea in the
category of mental processes.
Revised Guidance Step 2A, Prong 2
Although claim 1 recites an abstract idea, it would still be patent-
eligible if “the claim as a whole integrates the recited judicial exception into
a practical application of the exception.” Revised Guidance, 84 Fed. Reg. at
54. “A claim that integrates a judicial exception into a practical application
will apply, rely on, or use the judicial exception in a manner that imposes a
meaningful limit on the judicial exception.” Id. The analysis of whether a
claim integrates a judicial exception into a practical application includes
“[i]dentifying whether there are any additional elements recited in the claim
beyond the judicial exception(s)” and “evaluating those additional elements
individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
One of the exemplary considerations indicating that an additional
element may integrate an exception into a practical application is “[a]n
additional element [that] reflects an improvement in the functioning of a
computer, or an improvement to other technology or technical field.” Id.
at 55.
Here, claim 1 as a whole integrates the recited abstract idea (mental
processes) into a practical application. As discussed above, in addition to the
steps ((A), (B), and (C)) that can practically be performed in the human
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mind, claim 1 recites steps (D) through (G): “altering a side-chain rotamer
conformation . . . ,” “generating a plurality of sets of clusters . . . ,”
“grouping respective mutated polypeptide structures . . . ,” and “determining
a free energy estimate or configurational entropy . . . .” Claim 1.
Appellant’s Specification states that “[p]rotein engineering frequently
involves investigating the properties of a known wild-type sequence, making
mutations in a protein of known sequence and structure, and evaluating the
effects of these mutations on properties such as protein fold stability, or
protein binding.” Spec. ¶ 4. For example, to optimize the binding coefficient,
antigen specificity, or thermostability of an antibody, “a protein engineer
may study the thermodynamically relevant structural configurations of the
residues of the wild-type antibody, and on the basis of these results, elect to
mutate one or more residues of the antibody thereby causing the protein
sequence to change.” Id. ¶ 5. “[K]nowledge of the ensemble of
thermodynamically relevant protein structures for a given primary sequence
facilitates the identification of those substitutions that will lead to a protein
having more desirable physical characteristics.” Id. ¶ 3.
The Specification discusses two known, general approaches to
determining thermodynamically relevant structures, one of which “is limited
because low free energy states distinct from the ground state are common,
and can profoundly affect polymer behavior” and the other of which
produces thermodynamic averages that “are often inaccurate, and the sheer
size of the generated ensembles make detailed structural analysis
challenging.” Id. ¶¶ 6, 7. The Specification also reviews several published
approaches, and their limitations. Id. ¶¶ 8–13.
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The Specification states that the disclosed “methods for identifying
the thermodynamically relevant configurations of a polymer or polymer
region . . . combine configurational sampling and structural clustering
algorithms in novel ways to identify sets of polymer configurations that are
mutually distinct, and have free energies close to the thermodynamic ground
state.” Id. ¶ 15. The Specification states that the disclosed methods “are
capable of analyzing both residue side chain and residue backbone structural
variability, and doing so in a coupled fashion when desired.” Id.
Thus, the Specification describes the disclosed, and claimed, method
as improving on known methods of modeling the effect of mutations on the
structure and thermodynamic stability of a protein. The Specification states
that such modeling is useful in protein engineering in order to determine
which mutations are likely to have a desired effect on a protein’s properties;
e.g., the binding coefficient, antigen specificity, or thermostability of an
antibody.
We therefore agree with Appellant that the claimed method represents
“an improvement to a technical field or technical fields, namely protein
engineering” and “rational protein design and modeling.” Appeal Br. 14.
Thus, the claimed method, as a whole, is not “directed to . . . [a] patent-
ineligible concept.” Alice, 573 U.S. at 217. The same analysis applies to
independent claims 44 and 45. See id. at 226 (holding that claims to a
computer system and computer-readable medium were not meaningfully
distinguished from claims to a method).
The Examiner reasons that
[t]here are no positive process limitations recited in the claim
for actually using the information produced by the abstract idea
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outside of the computer (e.g. a real-world practical application
or solution to a problem). The claimed method does not require
anything more than generating information about in silico
coordinates of a molecule that satisfy certain criteria.
Ans. 6–7.
We do not agree that a physical step, such as actually making a mutant
protein, is required in order for the claimed method to constitute a practical
application of the recited mental processes. See, e.g., McRO, Inc. v. Bandai
Namco Games Amer., Inc., 837 F.3d 1299, 1315 (Fed. Cir. 2016) (“The
claimed process uses a combined order of specific rules that renders
information into a specific format that is then used and applied to create
desired results. . . . While the result may not be tangible, there is nothing that
requires a method ‘be tied to a machine or transform an article’ to be
patentable.”).
As discussed above, the Specification states that, in order to optimize
the physical properties of a protein, protein engineers first determine the
likely effect of different mutations on the structure and thermodynamic
properties of the protein, using methods such as the one defined by claim 1.
See Spec. ¶¶ 3–5. The Specification states that different approaches to this
problem have been developed, and several approaches have been published
in technical journals. Id. ¶¶ 6–13. Thus, the evidence shows that those
skilled in the art recognize the practical value of modeling the effect of a
mutation on a protein, even if the “real world” consequence is to rule out—
and therefore not make—certain mutant proteins because a mutation is
predicted to have an undesirable effect on the resulting protein.
In summary, we reverse the rejection of independent claims 1, 44, and
45 under 35 U.S.C. § 101. Claims 4, 5, 7, 9–15, 18, 19, 22, 23, 27–30, 36,
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38, 40, and 41 depend from claim 1 and we therefore reverse the rejection of
these claims as well, for the reasons discussed above.
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 4, 5, 7,
9–15, 18,
19, 22, 23,
27–30, 36,
38, 40, 41,
44, 45
101 Eligibility 1, 4, 5, 7,
9–15, 18,
19, 22, 23,
27–30, 36,
38, 40, 41,
44, 45

REVERSED