Ex Parte Ohrn et al

Patent Trial and Appeal Board

Nov 20, 2017

13822231 (P.T.A.B. Nov. 20, 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.
13/822,231 06/03/2013 Anders Ohrn 069480-5007-US 4953
43850 7590 11/22/2017
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
11/22/2017 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 GREGORY LAKATOS1
Appeal 2017-003914
Application 13/822,231
Technology Center 1600
Before JOHN G. NEW, RICHARD J. SMITH, and
DEVON ZASTROW NEWMAN, Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
appellants state that the real party-in-interest is Perceptive Credit
Opportunities Fund, L.P. App. Br. 3.
Appeal 2017-003914
Application 13/822,231
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 1, 5, 6, 9, 13, 14, 19, 20, 24, and 29-
33 as unpatentable under 35 U.S.C. § 101 as being directed to nonstatutory
subject matter.
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
NATURE OF THE CLAIMED INVENTION
Appellants’ invention is directed to a method of determining changes
in a first set of residues, n, due to changes in a second set of residues, r2, in a
protein system by optimizing a quality function, Q, by modifying one or
more properties of n and r2 in a constrained environment, in which all
degrees of freedom of the system except those directly involved in the
potential coupling between ri and r2 are removed. Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A computer implemented method of determining changes
in a property value of a first set of residues n due to
perturbations2 in a second set of residues /'2 in a protein system
22 Appellants’ Specification defines “perturbation” as:
A perturbation can be any change to any property of a residue.
For example, a perturbation can be a change in structure (e.g., a
change in one or more dihedral angles, bond angles or bond
lengths, in any combination), amino acid type (i.e., a mutation),
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Application 13/822,231
comprising one or more proteins, the protein system comprising
n and n, the method comprising:
for each respective perturbation pi in a first set of
perturbations Pi = {pi, . . . , pn}, wherein n is a user-defined
number of perturbations of value 2 or greater, performing the
method of:
(a) applying the respective perturbation pi to /'2, wherein
the respective perturbation is an alteration to the structure of one
or more residues of i%
(b) optimizing, responsive to the applying (a) and using an
atomistic force field for the entire protein system, a quality
function Q by modifying the conformation of residues of n and
r2 in a constrained environment in which the backbone of all
residues in the protein system apart from the residues in /'2 and n
are fixed during the optimization and in which Cp atoms of all
residues, other than glycine residues and proline residues, in the
protein system apart from the residues in /'2 and n are fixed
during the optimization and, wherein the quality function Q
comprises a free energy term for n and rp, and
(c) applying, upon completion of the optimizing (b), a
measure M to n thereby providing a physical property value v; of
ri, wherein the physical property value is a side-chain
conformation value, a backbone conformation value, or a
rotamer conformation value, and wherein the measure M
comprises an enumeration of the residues in n that exhibit an
altered property after application of one or more perturbations to
the residues of /'2 and optimization of Q, thereby obtaining a first
set of property values Vi = {vi, . . ., vn} for n, and thereby
the model used to represent a residue or the model used to
represent the interaction between the residue and its
environment.
Spec. 22.
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Application 13/822,231
determining changes in the property values of n due to
perturbations to n, wherein the method is performed on a
computer system.
App. Br. 20 (Claims App’x).
ISSUES AND ANALYSES
We decline to adopt the Examiner’s findings of fact and conclusions
that the appealed claims are directed to nonstatutory subject matter. We
address the arguments raised by Appellants below.
Issue
Appellants argue, inter alia, that the Examiner erred because the
claims are not directed to a judicial exception. App. Br. 11.
Analysis
The Examiner finds the claims are directed to processing information
through mathematical correlations and converting one form of numerical
representation into another and, as such, are directed to an abstract idea that
is a judicially-created exception to 35 U.S.C. § 101. Final Act. 3.
Specifically, the Examiner finds: (1) the claims do not include
additional elements that are sufficient to amount to significantly more than
the judicial exception; (2) the claims do not recite inventive steps outside of
data manipulation, or improvements to the functioning of the computer
itself; and (3) there are no meaningful limitations in the claims, beyond
generally linking the use of an abstract idea to a particular technological
environment, which transform the judicial exception into a patent-eligible
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Application 13/822,231
application such that the claim amounts to significantly more than the
exception itself. Final Act. 3-4. Furthermore, the Examiner finds that the
claims do not purport to improve the functioning of the computer itself and,
therefore, do not provide significantly more than a generic computer upon
which the claimed method steps are executed. Id. at 4.
Appellants point to the test set forth by the Supreme Court for subject
matter eligibility of a claimed method in Alice Corporation Pty. Ltd. v. CIS
Bank International, 134 S.Ct. 2347 (2014). Appellants assert that the two-
part Alice test requires the Examiner to: (1) determine whether the claim is
“directed to” a judicial exception, e.g., an abstract idea; and, (2) if so, to
determine whether any element, or combination of elements, in the claim is
sufficient to ensure that the claim amounts to significantly more than the
judicial exception. App. Br. 10. Furthermore, Appellants point to our
reviewing court’s further holding that, under the first prong of the Alice test,
“[t]he ‘directed to’ inquiry ... cannot simply ask whether the claims involve
a patent-ineligible concept.” Id. (quoting Enflsh, LLC. v. Microsoft Corp.,
822 F.3d 1327, 1334-35 (Fed. Cir. 2016) (emphasis in original), also citing
Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66,
71 (2012) (“For all inventions at some level embody, use, reflect, rest upon,
or apply laws of nature, natural phenomena, or abstract ideas”)). Rather,
Appellants assert, the question is whether, “considered in light of the
specification ... [the claims’] ‘character as a whole is directed to excluded
subject matter.” Id. (emphasis in original) (quoting Internet Patents Corp. v.
Active Networks, Inc., 790 F.3d 1343, 1346 (Fed. Cir. 2015).
Appellants argue that the claims on appeal are directed to a complex
method for modeling a protein system that includes meaningful limitations
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including: (1) applying a set of perturbations P\ to a set of residues n,
where the perturbations are alterations to the structure of the residues; (2)
optimizing a quality function Q, using an atomistic force field by modifying
the conformation of residues n and V2 in a constrained environment; (3) a
constrained environment includes fixed backbones and Cp residues for all
residues in the protein system other than residues n and r% (4) the quality
function Q includes a free energy term for n and i% and (5) application of
measure M to n to provide a side-chain conformation value, a backbone
conformation value, or a rotamer conformation value of n. App. Br. 11. As
such, Appellants argue, the claims do not seek to tie up all methods of
processing information through mathematical correlations and converting
one form of numerical representation into another, as found by the
Examiner. Id.
More specifically, Appellants contend that their claimed method does
not read on protein modeling that applies perturbations other than those
altering the structure of one or more residues, nor does it read on protein
modeling that optimizes a quality function other than by using an atomistic
force field. App. Br. 12. Appellants assert that their method does not read
on protein modeling by which the backbones of all residues are not fixed
during optimization or where the Cp atoms of all residues are not fixed
during optimization, even if the backbones of residues are fixed. Id.
Appellants also argue that their method does not read on protein modeling
by which the quality function does not include a free energy term for at least
two residues or where a measure is applied to provide a side-chain
conformation value, a backbone conformation value, or a rotamer
conformation value for a set of residues. Id. Therefore, Appellants argue,
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claim 1 does not preclude others from atomic modeling of a protein system
using conventional methods; rather, the claimed method is a specific
solution to a problem in the rational protein design and modeling arts that
significantly reduces the computational resources required for protein
modeling. Id.
It is Appellants’ contention, furthermore, that, when analyzed under
the framework established by the Supreme Court in Alice, the claimed
method is patentable because it is not directed to an abstract idea and
includes significantly more than any of the enumerated judicial exceptions.
App. Br. 13, 16. Specifically, Appellants point to our reviewing court’s
holding in Enfish that: “claims directed to software, as opposed to hardware,
are [not] inherently abstract .... Software can make non-abstract
improvements to computer technology.” Id. at 13 (quoting Enfish, 822 F.3d
at 1335-36).
According to Appellants, claim 1 is patent eligible because, as with
the claims in Enfish, it is drawn to an improvement in computer
functionality. Specifically, claim 1 allows for dramatically faster modeling
of coupling interactions between residues in a protein system. Id.
Appellants dispute the Examiner’s finding, therefore, that claim 1 is directed
to a method for “processing information through mathematical correlations”
and/or “converting one form of numerical representations into another.” Id.
at 14. To the contrary, Appellants argue, their claims are focused on a
specific solution to a problem in the rational protein design and modeling
arts, i.e., that conventional methods for modeling protein interactions are
computationally taxing. Id. Appellants assert that, because claim 1 is
directed to this specific method, which improves computer functionality by
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allowing faster modeling or residue interactions in a protein system rather
than merely processing information through mathematical correlations and
converting numerical representations, the character of the claim as a whole
is not directed to excludable subject matter. Id. at 15.
Appellants also argue that claim 1 includes more than merely the
judicial exceptions enumerated in Alice. App. Br. 16. Appellants assert that
the “significantly more” analysis set forth in Alice turns on whether
performance of a particular claim element, and its combination with any
additional claim element, was a “well-understood, routine, conventional
activity previously engaged in by scientists in the field.” Id. (quoting
USPTO, Update: Memorandum - Recent Subject Matter Eligibility
Decisions 4, https://www.uspto.gov/sites/default/files/documents/ieg-may-
2016-ff.pdf (2016) (“May 16, 2016, Update”)).
Appellants contend that claim 1 includes significantly more because it
has an “inventive concept” that applies the alleged judicial exception of
“processing information through mathematical correlations and converting
one form of numerical representation into another” in a meaningful way that
provides an improvement in the field of rational protein design and
modeling. App. Br. 16. Appellants assert that, by improving computer
functionality, the claimed invention significantly reduces the time and
computing resources required to model coupling interactions between pairs
of residues in a protein system, as explained supra. Id. Appellants assert
that their claimed method was thus not a well-understood, routine, or
conventional activity previously engaged in by scientists in the field. Id.
The Examiner responds that Appellants adduce no evidence that the
functionality of the computer-implemented method recited in their claims-as
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Application 13/822,231
opposed to the number of steps executed by the computer-is at all affected
by the method steps. Ans. 2. The Examiner observes that a computer that
runs “shorter lines of code is obviously faster, but does not improve
functionality of the computer.” Id.
The Examiner finds that the method recited by Appellants’ claims are
drawn to processing information and converting one form of numerical
representation into another by organizing information through
“mathematical concepts such as mathematical algorithms, mathematical
relationships, mathematical formulas, and calculations.” Ans. 2. Therefore,
the Examiner finds the steps of the claimed method are directed to an
abstract idea that is a recognized judicial exception and not patentable. Id.
We are not persuaded that the Examiner has established a prima facie
case that the claims are not patentable under the exceptions to 35 U.S.C. §
101. Appellants do not dispute that the claims are directed to a computer-
implemented method, i.e., a modeling program of determining changes in a
set of amino acid residues in a protein system resulting from perturbations
made to a second set of residues under rigidly-defined conditions. See
Abstr. The question before us, then, is whether such a modeling program,
executable on a standard computer, is patentable under § 101.
Section 101 defines patent-eligible subject matter as “any new and
useful process, machine, manufacture, or composition of matter, or any new
and useful improvement thereof,” subject to the other limitations of the
Patent Act. 35 U.S.C. § 101. The courts have created judicial exceptions to
the literal scope of § 101, viz.: “Laws of nature, natural phenomena, and
abstract ideas are not patentable.” Alice, 134 S.Ct. at 2354 (quoting Ass ’n
for Molecular Pathology v. Myriad Genetics, Inc., 133 S.Ct. 2107, 2116
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(2013)). The Examiner finds that Appellants’ claims fall under the abstract
idea exception.
The framework set forth by the Supreme Court in Alice has been
summarized by our reviewing court in McRO, Inc. v. Bandai Namco Games
America Inc., 837 F.3d 1299, 1311-12 (Fed. Cir. 2016). In Alice, the Court
applied a two-step framework for analyzing whether claims are patent
eligible. First, the panel must determine whether the claim at issue is
“directed to” a judicial exception, such as an abstract idea, including
mathematical formulae. See Alice, 134 S.Ct. at 2355; Gottschalk v. Benson,
409 U.S. 63, 64 (1972). The abstract idea exception prevents patenting a
result where “it matters not by what process or machinery the result is
accomplished.” O’Reilly v. Morse, 56 U.S. 62, 113 (1853). However, we do
not automatically assume that such claims are directed to patent ineligible
subject matter because “all inventions at some level embody, use, reflect,
rest upon, or apply laws of nature, natural phenomena, or abstract ideas.”
Mayo, 566 U.S. at 71 (2012). Instead, we analyze “the claims ... in their
entirety to ascertain whether their character as a whole is directed to
excluded subject matter.” Internet Patents Corp., 790 F.3d at 1346. If we
determine the claims are directed to an abstract idea, then the inquiry
proceeds to the second step of the Alice framework. Alice, 134 S.Ct. at
2355.
In step two, we consider whether the claims contain an “inventive
concept” sufficient to “transform the nature of the claim into a patent-
eligible application.” Alice, 134 S.Ct. at 2355 (quotation omitted). To do
so, we must look to both the claim as a whole and the individual claim
elements to determine whether the claims contain “an element or
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combination of elements that is ‘sufficient to ensure that the patent in
practice amounts to significantly more than a patent upon the [ineligible
concept] itself.’” Id. (quoting Mayo, 566 U.S. at 71-72) (alteration in
original).
The Examiner finds that Appellants’ claims are drawn to “processing
information and converting one form of numerical representation into
another by organizing information through mathematical concepts such as
mathematical algorithms, mathematical relationships, mathematical
formulas, and calculations” and are therefore drawn to an ineligible abstract
idea. Ans. 2. Claims have been held ineligible by our reviewing court as
being directed to an abstract idea when they merely collect electronic
information, display information, or embody mental processes that could be
performed by humans. Thales Visionix Inc. v. United States, 850 F.3d 1343,
1346^17 (Fed. Cir. 2017) (citing Elec. Power Grp., LLC v. Alstom S.A., 830
F.3d 1350, 1353-54 (Fed. Cir. 2016) (collecting cases). However, our
reviewing court has also admonished us that we “must be careful to avoid
oversimplifying the claims” by looking at them generally and failing to
account for the specific requirements of the claims.” McRO, 837 F.3d at
1313 (citing In re TLI Commc’ns LLC Patent Litig., 823 F.3d 607, 611 (Fed.
Cir. 2016)).
Furthermore, a central concern of Section 101, and its judicially-
created exceptions, is the prevention of preemption, by which claims are not
directed to a specific invention, but rather improperly monopolize “the basic
tools of scientific and technological work.” McRO, 837 F.3d at 1314 (citing
Alice, 134 S.Ct. at 2354 (quoting Myriad, 133 S.Ct. at 2116)). The abstract
idea exception has been applied to prevent patenting of claims that abstractly
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cover results where “it matters not by what process or machinery the result is
accomplished.” Id. (citing O’Reilly, 56 U.S. at 113); Mayo, 566 U.S. at 84)).
We must therefore look to whether the claims on appeal focus on a specific
means or method that improves the relevant technology, or are instead
directed to a result or effect that is itself the abstract idea and that merely
invokes generic processes and machinery. Id. (citing Enflsh, LLC v.
Microsoft Corp., 822 F.3d 1327, 1336 (Fed. Cir. 2016); RapidLitig. Mgmt.
Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1048 (Fed. Cir. 2016)).
In the appeal before us, the claims are limited to rules with specific
requirements. Specifically, Appellants’ claim 1 requires:
[ ] applying the respective perturbation pi to n, wherein the
respective perturbation is an alteration to the structure of one or
more residues of ry
[ ] optimizing, responsive to the applying (a) and using an
atomistic force field for the entire protein system, a quality
function Q by modifying the conformation of residues of n and
r2 in a constrained environment in which the backbone of all
residues in the protein system apart from the residues in ly and n
are fixed during the optimization and in which Cp atoms of all
residues, other than glycine residues and proline residues, in the
protein system apart from the residues in /'2 and n are fixed
during the optimization and, wherein the quality function Q
comprises a free energy term for n and ry, and
[ ] applying, upon completion of the optimizing[ ], a measure M
to ri thereby providing a physical property value v; of n,
wherein the physical property value is a side-chain
conformation value, a backbone conformation value, or a
rotamer conformation value, and wherein the measure M
comprises an enumeration of the residues in n that exhibit an
altered property after application of one or more perturbations
to the residues of n and optimization of Q, thereby obtaining a
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first set of property values V\ = {vi,. . vn} for n, and thereby
determining changes in the property values of n due to
perturbations to /% wherein the method is performed on a
computer system.
The specific, claimed features of these rules thus permit the improvement
realized by the invention, i.e., an improved method of determining the
effects of perturbations on one set of amino acid residues /'2 in a protein
upon another set of residues n, under certain conditions and assumptions.
SeeMcRO, 837 F.3d at 1313.
Claim 1 is thus focused on a specific articulated improvement in
protein modeling, i.e., “determin[ing] ... positions in a polypeptide (or
protein) that are likely to be intrinsically coupled, irrespective of the amino
acid type at that position, or the coupling between specific amino acids in
the polypeptide sequence.” Spec. ^ 6. We are therefore not persuaded by
the Examiner’s finding that that the claims simply use a computer as a tool
to automate generic conventional activity, i.e., “converting one form of
numerical representation into another by organizing information through
mathematical concepts.” See Ans. 2. Rather, the novel inventive concept of
the claimed method is a new manner of predicting alterations in one set of
amino acid residues as a result of perturbations to a second set of residues
under a specified set of conditions and assumptions. Although the rules
recited in claim 1 are embodied in computer software that can be processed
by a general-purpose computer, the Examiner adduces no evidence that the
process required by the claims is the same as any process previously used in
protein modeling and conducted by similar or other means. Indeed, the
Examiner provides no evidence that the method recited in claim 1 of
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quantitatively determining how perturbations to one set of amino acid
residues affects another set in a protein system has ever been practiced by
those of skill in the art of protein structure and design, whether with a
computer, paper and pencil, or mentally. Consequently, and unlike cases
such as Alice, the Examiner has not shown that the computer-automated
method of claim 1, and any prior method, were carried out in the same way.
See Alice, 134 S.Ct. at 2356; see also Parker v. Flook, 437 U.S. 584, 585-86
(1978); Bilski v. Kappos, 561 U.S. 593, 611 (2010); McRO, 837 F.3d at
1314.
We therefore find the claims before us to be distinguishable from
those in Alice and related cases, in which the computer-implemented method
was responsible for merely “organizing [existing] information into a new
form” or carrying out a previously-known and fundamental economic
practice. McRO, 837 F.3d at 1315 (citing Digitech Image Techs., LLC v.
Elecs. for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014f Alice, 134
S.Ct. at 2356). Appellants’ claimed method uses a combined order of
specific rules that render information into a specific format that is then used
and applied to create desired results: a determination of the effect upon an
amino acid reside n when another residue ri is perturbed. We acknowledge
that the results of Appellants’ claimed method are not, in themselves,
tangible, but there is nothing that requires a method “be tied to a machine or
the transformation of an article” to be patentable. Bilski, 561 U.S. at 603
(discussing 35 U.S.C. § 100(b)).
Nor do we find that Appellants’ claims would preempt any judicially-
created exception to Section 101. Rather, Appellants’ claims are directed to
a specific, computer-implemented process of protein modeling with specific
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rules directed to that end. Appellants have explained, as we have related
supra, why the specific method recited in the claims does not “[improperly
monopolize] the basic tools of scientific and technological work” (see Alice,
134 S.Ct. at 2354) and the Examiner has not adduced any findings to rebut
Appellants’ arguments. See App. Br. 12.
In summary, then, we find that Appellants’ claims are directed and
limited to a specific process which, though perhaps producing an intangible
result, are directed not to a computer-implemented version of a previously
known and familiar method re-organization of data into a new form or a
fundamental economic process, but rather to a method of calculating a result
within the context of a specific set of limiting rules and assumptions in a
method that is fundamentally new and inventive. We consequently conclude
that Appellants’ claimed method does not fall within a judicially-created
exception to Section 101. See McRO, 837 F.3d at 1315. Accordingly, we
reverse the Examiner’s rejection of the claims.
DECISION
The Examiner’s rejection of claims 1, 5, 6, 9, 13, 14, 19, 20, 24, and
29-33 as unpatentable under 35 U.S.C. § 101 is reversed.
REVERSED
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