Hiroshi Izumi et al.

Patent Trials and Appeals Board

Mar 15, 2021

2020003162 (P.T.A.B. Mar. 15, 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.
12/385,856 04/22/2009 Hiroshi Izumi 2009_0551A 2031
513 7590 03/15/2021
WENDEROTH, LIND & PONACK, L.L.P.
1025 Connecticut Avenue, NW
Suite 500
Washington, DC 20036
EXAMINER
DEJONG, ERIC S
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
03/15/2021 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):
eoa@wenderoth.com
kmiller@wenderoth.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte HIROSHI IZUMI, ATSUSHI OGATA, KAZUYUKI TAKEO,
and HIDEKI KOBAYASHI
____________

Appeal 2020-003162
Application 12/385,856
Technology Center 1600
____________

Before DONALD E. ADAMS, RYAN H. FLAX, and
TIMOTHY G. MAJORS, Administrative Patent Judges.

MAJORS, Administrative Patent Judge.

DECISION ON APPEAL
Appellant1 submits this appeal2 under 35 U.S.C. § 134(a) involving
claims to a conformational notation device and method, which claims have
been rejected for claiming non-statutory subject matter under 35 U.S.C.
§ 101. We have jurisdiction under 35 U.S.C. § 6.
We REVERSE.

1 “Appellant” refers to “applicant” as defined in 37 C.F.R. § 1.42(a).
Appellant identifies named inventor, Hiroshi Izumi as the real party-in-
interest. Appeal Br. 2.
2 Appellant identifies as related our decision in Ex parte Izumi, Appeal 2016-
006277 (PTAB Apr. 27, 2017). Appeal Br. 2.
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STATEMENT OF THE CASE
Appellant’s “invention relates to a device and a method for simply
and more precisely analyzing conformations of pharmaceutically active
species.” Spec. 1. “[T]he present invention relates to a device and a method
for simply and more precisely notating a physical property value related to a
drug action and the like along with a conformational structure thereof.” Id.
According to the Specification,
an object [is] to provide conformation analysis device and
analysis method with which discrimination can be achieved even
if there is a subtle difference in a conformational structure, a
given molecule can be processed in a unified manner, and large-
scale computer processing can be performed.

Id. at 5. The Specification explains that with compounds having chirality
(e.g., biomolecules), spectroscopic measurement of such compounds using
vibrational circular dichroism (“VCD”) provides some structural and/or
conformation information, yet “a problem [is] that when there is a subtle
difference in the [conformational] structure, discrimination cannot be
achieved.” Id. at 2; see id. at 3–4 (explaining the limitations of determining
a conformation of compounds such as levofloxacin and ibuprofen when
applying VCD with conventional IUPAC notation rules). By way of
example, the Specification explains that, “although it was impossible to
compare conformations of active species of [the compound] Taxol based on
the conventionally used notations . . . according to the invention, it is
possible to easily compare a difference in the conformations of the
respective active species.” Id. at 7. Further, “by using the method in
combination with vibrational circular dichroism data, a conformational
structure having a large abundance ratio in a liquid phase state can be
extracted.” Id. at 7–8.
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Claims 17–24 are on appeal. Claim 17 is illustrative:
17. A conformation notation method comprising:
receiving, using a processor, a plurality of molecular models as
an input, each of the plurality of molecular models corresponding to a
different conformation of interest of a compound;
defining, using the processor, a conformational notation for each
molecular model from among a plurality of molecular models;
storing, in a database, each defined conformational notation by
linking the conformational notation to the corresponding molecular
model from among the plurality of molecular models; and
performing, using the processor, conformation analysis for each
of the stored conformational notations,
wherein the defining the conformational notation for each
molecular model includes
(i) separating the molecular model into one or more
fragments,
(ii) determining a dihedral angle in accordance with an order
of a position number determined by the IUPAC
Nomenclature and a selection of a substituent group or an
atom taking first priority in accordance with the priority
rule of the IUPAC Nomenclature in each chemical binding
site,
(iii) assigning, as a classification of the dihedral angle, one of
a plurality of codes corresponding to six segments
obtained by dividing 360 degrees into the six segments,
(iv) putting, as the classification of the dihedral angle, one of a
plurality of codes corresponding to twelve segments
obtained by adding two kinds of codes corresponding to α
(clockwise) and β (counterclockwise) to each of the six
segments in a case where conformations that should be
judged as different from each other belong to a same
classification indicated by any one of the plurality of codes
corresponding to the six segments in a chemical binding
site;
(v) putting a code corresponding to a chemical bond of
interest of the conformational notation or notating by
using a notation in which a prefix for correctly indicating
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only a position of the dihedral angle and the code are
combined, and
(vi) omitting unnecessary notations in a case where a chemical
structure is capable of being uniquely determined even if
a part of the notations of the chemical bond is omitted
when notating a conformation of a fragment,
wherein the conformational notation for each molecular model
from among the plurality of molecular models is defined so that each
of the conformation notations is unique,
wherein the performing the conformation analysis for each of the
stored conformational notations includes
(i) extracting the conformational notation from the database,
(ii) creating a molecular model from the extracted
conformational notation,
(iii) performing geometry optimization and frequency
calculation for the created molecular model,
(iv) determining an energy value or another physical property
value of the resulting geometry optimized molecular
model, and
(v) storing the determined energy value or the other physical
property value in the database by linking the stored value
to the corresponding molecular model,
wherein, when the geometry optimization for the molecular
model created from the extracted conformational notation requires that
the molecular model corresponding to the extracted conformational
notation be changed, the defining the conformational notation for the
molecular model corresponding to the extracted conformational
notation is repeated, and
wherein the conformational notation method further comprises:
receiving, in a case where an energy value or another
physical property is observed for the compound to be analyzed
and the observed value is linked to each of the plurality of
molecular models corresponding to the compound to be
analyzed, the observed energy value or the observed other
physical property being obtained using vibration circular
dichroism analysis or X-ray crystal structure analysis;
extracting, from the database, the conformational notation
for each molecular model from among the plurality of molecular
models:
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performing homology analysis using (i) the received
observed energy value or the received observed other physical
property and (ii) the extracted conformation notion3 [sic] for each
molecular model from among the plurality of molecular models;
and
outputting, to a display, the results of the homology
analysis and the extracted conformational notation for each
molecular model from among the plurality of molecular models.
Appeal Br. 17–19. The other claims on appeal stand or fall with claim 17 on
this record. See 37 C.F.R. § 41.37(c)(iv).
Appellant seeks review of the Examiner’s rejection of claims 17–24
for claiming patent ineligible subject matter under 35 U.S.C. § 101. Final
Act.4 3–5; Ans. 3–5.
ANALYSIS
The Examiner “bears the initial burden . . . of presenting a prima facie
case of unpatentability.” In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir.
1992). Considering the argument and evidence of record, we conclude that
the Examiner has not met the burden of showing prima facie unpatentability
of the pending claims under § 101. We explain below.
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101. The
Supreme Court has, however, held that § 101 includes implicit exceptions—
laws of nature, natural phenomena, and abstract ideas—which are not
patent-eligible. See Alice Corp. v. CLS Bank Int’l, 573 U.S. 208, 216
(2014); Bilski v. Kappos, 561 U.S. 593, 601 (2010). In January 2019, the

3 It appears this term should be “notation” consistent with the remainder of
the claim.
4 This citation refers to the Examiner’s Final Rejection dated January 24,
2019. The substance of the rejection is repeated in the Examiner’s Answer
(hereafter “Ans.” or “Answer”) on appeal, entered February 28, 2020.
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Patent Office issued the 2019 Revised Patent Subject Matter Eligibility
Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019) (“2019 Guidance”). The 2019
Guidance addresses the manner in which the Office is to apply the § 101
case law.5 Office personnel, including examiners and the Board, are
required to adhere to the 2019 Guidance. 2019 Guidance at 51. The 2019
Guidance sets forth a four-part analysis for determining whether a claim is
patent eligible under § 101. The four parts are referred to as Step 1, Step 2A
Prong 1, Step 2A Prong 2, and Step 2B. Id. at 53–56.
With respect to the present rejection, we take special note of Prong 1
and Prong 2 of Step 2A, which relate to determining whether a claim recites
patent-ineligible subject matter and, if so, whether it integrates such into a
practical application, which together determine if the claim is directed to
patent-ineligible subject matter, e.g., an abstract idea. On this record,
because the Examiner did not directly and persuasively address the inquiries
under Step 2A, particularly Step 2A’s Prong 2, we conclude that the
Examiner failed to make a threshold showing sufficient to support the
rejection.6 Reversal of the rejection is, therefore, warranted.
1. 2019 Guidance Step 2A Prong 1
Under “Step 2A Prong 1,” the Office evaluates “whether the claim
recites a judicial exception, i.e., an abstract idea, a law of nature, or a natural

5 The Office issued a further update in October 2019. October 2019 Patent
Eligibility Guidance Update, 84 Fed. Reg. 55942 (Oct. 18, 2019).
6 The 2019 Guidance became effective on January 7, 2019. The § 101
rejection on appeal was entered weeks later, on January 24, 2019. The
rejection, however, neither cites the guidance nor expressly addresses the
claims under the guidance’s specific, step-wise framework. The Examiner
briefly mentions a step of the guidance in the Answer’s Response to
Argument section, but that mention is merely characterizing an argument
raised by Appellant. Ans. 6.
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phenomenon.” 2019 Guidance at 54; see Alice, 573 U.S. at 216;7 Bilski, 561
U.S. at 601–602.8 The 2019 Guidance identifies the following as a sub-
group of abstract ideas: “Mental processes—concepts performed in the
human mind (including an observation, evaluation, judgment, opinion).”
2019 Guidance at 52 (footnotes omitted).
The Examiner cites to certain claimed steps (of claim 17) that involve
a processor and finds such steps do not “go beyond routine computer
operations.” Final Act. 4. For the step involving “assigning” classifications,
the Examiner finds that this step “appears to require no more than an artisan
determining what common structural characteristics are present” and this
allegedly “fail[s] to delineate anything other than routine activity practicable
in or appreciated by the mind of an artisan.” Id. The Examiner, upon
“taking the claims as a whole,” finds that the claims encompass an “abstract
procedure of inspecting and characterizing” molecular models. Id. at 4–5
(emphasis added). On this record, we understand the Examiner to find that
at least some of the claim limitations recite abstract mental processes.9 The
Examiner’s findings, therefore, satisfy Step 2A’s Prong 1 in that at least
some recited steps are alleged to encompass a mental process and, thus, an

7 In Alice, a method of exchanging financial obligations between parties
using a third-party intermediary to mitigate settlement risk was held to claim
an abstract idea. Alice, 573 U.S. at 219.
8 In Bilski, a method of hedging risk was deemed an abstract idea. Bilski,
561 U.S. at 611.
9 The Examiner also describes the claims as including “abstract
mathematical and algorithmic operations,” but the Examiner does not
identify what limitation (or limitations) the Examiner believes recite
mathematical concepts. Final Act. 5–6; 2019 Guidance at 52 (explaining the
Step 2A, Prong 1 analysis, and that mathematical concepts, certain methods
of organizing human activity, and mental processes are three recognized
groupings identified by courts as abstract ideas).
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abstract idea. Appellant’s contentions to the contrary are not persuasive.
See Appeal Brief. 9–10.
2. 2019 Guidance Step 2A Prong 2
Turning to “Step 2A Prong 2,” the Office evaluates whether “the
claim as a whole integrates the recited judicial exception into a practical
application.” 2019 Guidance at 54. If the judicial exception (i.e., abstract
idea) is so integrated, then the claim is not “directed to” a judicial exception
and is instead subject matter that is eligible for patenting. Id. In that case,
the § 101 eligibility inquiry ends and does not proceed to Step 2(B) (i.e.,
whether the claim includes an “inventive concept” beyond the judicial
exception). Id. at 56 (internal quotation marks and footnotes omitted).
“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, such that the claim is
more than a drafting effort designed to monopolize the judicial exception.”
Id. at 54; see Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S.
66, 78 (2012). The 2019 Guidance requires the analysis proceed by first
“[i]dentifying whether there are any additional elements recited in the claim
beyond the judicial exception(s),” then “evaluating those additional elements
individually and in combination to determine whether they integrate the
exception into a practical application.” 2019 Guidance at 54–55.
The 2019 Guidance lists non-exhaustive, exemplary considerations
tending to indicate that a judicial exception, such as an abstract idea, has
been integrated into a practical application. Those considerations include:
An additional element reflects an improvement in the
functioning of a computer, or an improvement to other
technology or technical field;
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an additional element that applies or uses a judicial
exception to effect a particular treatment or prophylaxis for a
disease or medical condition; [and]
an additional element effects a transformation or reduction
of a particular article to a different state or thing.
Id. at 55 (footnotes omitted).
The Examiner does not address Step 2A Prong 2 and the “integrate[d]
. . . into a practical application” analysis, except perhaps obliquely in
response to arguments made by Appellant. Appeal Br. 10–12. That missing
analysis is significant here.
Appellant argues the claims, as amended on July 23, 2017, are
directed to “an improvement in computer-related technology in the fields of
vibrational circular dichroism (VCD) analysis and X-ray crystal structure
analysis.” Id. at 9 (emphasis omitted); see also id. at 12 (“[U]nder Revised
Step 2A, the presently claimed invention provides a combination of elements
that reflect an improvement in the technical fields of VCD analysis and X-
ray crystal structure analysis . . . [and thus] the alleged abstract idea . . . is
integrated into a practical application.”). Further, citing its declarant’s
testimony10 and other evidence, Appellant contends the improvement in
determining 3-D molecular conformations provided by the claimed method
and device is shown in several technical publications, and for numerous
compounds—revealing conformations that could not be determined with
conventional spectroscopic techniques. Id. at 13–14 (arguing that the
claimed method revealed for the first time various in-solution molecular
conformations for thalidomide, malathion, Taxol, levofloxacin, and
ibuprofen).

10 See Declaration of Hiroshi Isumi, dated October 9, 2018 (of record, and
attaching several technical publications).
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The Examiner does not challenge Appellant’s evidence, nor dispute
that the invention provides a technological improvement in a technological
field. Instead, the Examiner asserts that Appellant “confused” the instant
rejection for subject matter eligibility with a “utility” rejection under § 101.
Ans. 6; Final Act. 7. We do not share that assessment of Appellant’s
argument here. To the contrary, as noted by Appellant, “the arguments
included in the Appeal Brief . . . are clearly based on the 2019 Revised
Patent Subject Matter Guidelines.” Reply Br. 3. And importantly, the
Examiner never provides a sufficient analysis on the key question whether
the amended claims, considering the limitations individually and as a whole,
integrate the alleged abstract idea into a practical application. The
Examiner’s single-sentence response that “appellant is only arguing features
of the judicial exception itself rather than additional elements that would
integrate said judicial exception into a statutory, practical application” falls
short. Ans. 7. For example, the Examiner has not explained on this record
why the amended claim language, now limiting and applying the claims to
molecular compounds and their properties determined with VCD or X-ray
crystal structural analysis, leaves the claims abstract and without
implementing such into a practical application.11

11 It is also not apparent from the rejection that the Examiner considered all
the limitations of the pending claims, including those added by amendment
in 2017, such as the added limitations related to VCD. Moreover, in the
May 28, 2019 Advisory Action, after Appellant pointed out that the
Examiner had not applied the 2019 Guidelines, the Examiner referred to a
“proposed” amendment with “newly presented limitations,” and stated that
the “argument and amendment are acknowledged but are not directed to the
claims currently of record.” Adv. Act. 1–2 (checking the box concerning
“proposed amendments” that “will not be entered”). But, there does not
appear to have been a proposed claim amendment pending at the time in
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Although true, as the Examiner suggests, limiting an abstract claim to
a certain field may not make it patent eligible. Ans. 7; Parker v. Flook, 437
U.S. 584, 588, 594–595 n.18 (1978). That prohibition is, however, more
likely implicated where the limitation appears to be a draftsperson’s artifice
and effort to still preempt the abstract idea itself. 2019 Guidance 55–56. It
is not apparent that concern is implicated here. Consistent with Appellant’s
position, the Specification repeatedly discusses the particular applicability
and improvement the invention is said to provide to VCD spectral analysis.
See, e.g., Spec. 2–8, 38, 41, 51. To the extent the pending claims do recite
one or more abstract ideas, it is not clear on this record that there is any
broad applicability and risk of preemption of those ideas outside the more
limited real-world measurement techniques described in the Specification
that are the focus of Appellant’s arguments.
The Examiner further responds that Appellant “previously presented
this [utility] argument in the previous appeal,” suggesting that the Board has
already considered, but rejected it. Ans. 6 (citing Appeal 2016-006277, slip
op. at 8–9); see id. at 8 (citing Appeal 2016-006277, slip op. at 6–8). The
Examiner is correct in noting, as the Board remarked in 2017, that simply
because a claimed invention is new and useful does not necessarily impart
patent eligibility. But the Examiner is incorrect in suggesting the Board
considered the same arguments Appellant is making now. First, the Office’s
2019 Guidance did not exist at the time of the earlier appeal. Second, the
claims have been amended to add subject matter the Board expressly noted
was missing at that time. Appeal 2016-006277, slip op. at 11 (observing the

2019—the appealed claims are those that were amended years before in July
2017, so it is unclear what claim language the Examiner was referring to in
the Final Rejection and Advisory Action.
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Specification’s support for the improvement and use of the invention in
three-dimensional fragment analysis when tied to VCD, but explaining that
“claim 17 does not recite use for VCD analysis, [and] Appellants have
identified no limitations specific to VCD analysis”). Third, we refused to
consider Appellant’s publication evidence about the alleged real-world
improvements provided by the claimed method because we determined that
evidence was submitted too late (id.); here, Appellant’s declaration evidence
and supporting publications was timely submitted and is of record. In short,
the Office’s analytical framework has evolved, and the claims and the
evidentiary record have changed, but the Examiner does not persuasively
address all limitations of the new claims and the new evidence according to
the Office’s new guidance.
For the above reasons, we conclude that the Examiner has not made a
sufficient showing on whether Appellant’s claims are (or are not) integrated
into a practical application, as explained under the Office’s 2019 Guidance,
Step 2A, prong 2. We, therefore, reverse the § 101 rejection on appeal.
CONCLUSION
In summary:
Claim(s)
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
17–24 101 Eligibility 17–24

REVERSED