Ex Parte Goddard et al

Patent Trial and Appeal Board

Jul 6, 2017

12944700 (P.T.A.B. Jul. 6, 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.
12/944,700 11/11/2010 William A. Goddard III P701-US 6245
72932 7590
Steinfl + Bruno LLP
155 N. Lake Ave. Ste 700
Pasadena, CA 91101
07/06/2017 EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
07/06/2017 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte WILLIAM A. GODDARD III, RAVINDER ABROL,
ISMET C. TANRIKULU, and ADAM R. GRIFFITH
Appeal 2017-0005601
Application 12/944,700
Technology Center 1600
Before RICHARD M. LEBOVITZ, DAVID COTTA, and
TAWEN CHANG, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to computer-operated methods
for predicting binding poses of a binding molecule to a target molecule. The
Examiner rejected the claims under 35 U.S.C. § 103 as obvious and under 35
U.S.C. § 101 as directed to a judicial exception to patent eligibility. We
have jurisdiction under 35 U.S.C. § 6(b). The rejections are affirmed.
STATEMENT OF THE CASE
Appellants appeal from the Examiner’s rejection of claims 1—5 and 8—
23. The claims stand rejected as follows:
1 The Appeal Brief (“Appeal Br.”) 2 lists California Institute of Technology
as the assignee and real-party-in-interest.
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1. Claim 1—5, 8—10, 18, 19, and 21—23 under 35 U.S.C. § 103(a) as
obvious in view of Cho et al. (Art E. Cho et al. , The MPSim-Dock
Hierarchical Docking Algorithm: Application to the Eight Trypsin Inhibitor
Cocrystals, 26 J. of Comput Chem48, 48—71 (2005) (“hereinafter “Cho”)),
Itai et al. (US 2006/0100789 Al, published May 11, 2006 (hereinafter
“Itai”)), and McConkey et al. (Brendan J. McConkey et al., The
Performance of Current Methods in Ligand-Protein Docking, 83 Current
Science No. 7, 845, 845—856 (2002) (hereinafter “McConkey”)). Final
Office Action (“Final Act.”) 7.
2. Claims 11—20 under 35 U.S.C. § 103(a) as obvious in view of Cho,
Itai, McConkey, and Hellinga et al. (US 2004/0229290 Al, published Nov.
18, 2004 (hereinafter “Hellinga”)). Id. at 11, 13.
3. Claims 1—5 and 8—23 under 35 U.S.C. § 101 as directed to patent
ineligible subject matter. Id. at 3.
Claim 1 is representative and reads as follows:
1. A computer-operated method for predicting binding
poses of a binding molecule, wherein the binding molecule is
adapted to be bound to a target molecule, the method
comprising the following computer-operated steps wherein a
computer performs the steps in single-processor mode or
multiple-processor mode:
providing at least one molecular pose for the binding
molecule;
clustering the at least one molecular pose into at least one
family, wherein the clustering is based on position of each
molecular conformation in the target molecule;
selecting, upon completion of all iterations of the
providing and the clustering, a family head for each family in
the at least one family based on geometric properties;
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selecting a full set or subset of families based on
interaction energy between each family head and the target
molecule; and
selecting a full set or subset of molecular poses from
among the molecular poses in the full set or subset of families
based on interaction energy between each molecular pose and
the target molecule;
wherein the interaction energy comprises total interaction
energy, polar interaction energy, and phobic interaction energy
and the molecular pose selecting comprises:
selecting a first set of molecular poses from among the
molecular poses in the full set or subset of families based on the
total interaction energy;
selecting a second set of molecular poses from among the
molecular poses in the full set or subset of families based on the
polar interaction energy; and
selecting a third set of molecular poses from among the
molecular poses in the full set or subset of families based on the
phobic interaction energy.
THE PERSON OF ORDINARY SKILL IN THE ART
When making a patentability determination under 35 U.S.C., we
consider the claims and the scope and content of the prior art to be directed
to one of ordinary skill in the art. Thus, a determination as to whether the
claims conform to the patentability requirements of 35 U.S.C. is made from
the perspective of one of ordinary skill in the art. In this case, the claimed
subject matter involves computer operated methods to predict binding poses
of a binding molecule to a target molecule. The method has steps of
selecting poses based on interaction energies and involves computer
modeling. The cited prior art includes patents, published patent applications,
and scientific journal articles in the fields of computer-aided methods for the
identification and characterization of ligand-protein interactions and energy
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scoring algorithms. Persons who publish in scientific journals typically are
scientists who have advanced degrees in the pertinent field (e.g., chemistry,
biology), such as masters and Ph.D. degrees. Accordingly, the person of
ordinary skill in the art pertinent to the claimed subject matter is a scientist,
familiar with the patent and scientific literature, who has (1) at least an
advanced degree in chemistry or biology and (2) experience in computer
protein-ligand modeling, determining energy interactions between
molecules, and performing energy computations. Such ordinary skilled
worker would have studied the interactions between proteins and ligands,
i.e., binding of molecules to targets.
OBVIOUSNESS REJECTION
Claim 1 is directed to a computer-operated method for predicting
binding poses of a binding molecule bound to a target molecule. A “pose” is
described in the Specification as a molecular “conformation” that takes place
when a binding molecule binds to the target molecule, such as when a ligand
binds to a protein. Spec. 1 3. The claimed method involves steps of
providing molecular poses for the binding molecule and clustering the poses
based “on position of each molecular conformation in the target molecule.”
The poses are clustered into at least one family. “A full set or subset of
molecular poses” is selected “based on interaction energy between each
molecular pose and the target molecule.” Appeal. Br., Claims App.
(emphasis added).
The interaction energy of the claims comprises: 1) total interaction
energy, 2) polar interaction energy, and 3) phobic interaction energy.
The molecular pose selecting comprises:
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A) “selecting a first set of molecular poses . . . based on the total
interaction energy,”
B) “selecting a second set of molecular poses . . . based on the polar
interaction energy,” and
C) “selecting a third set of molecular poses . . . based on the phobic
interaction energy.'1'’
The Specification defines total interaction energy as
a sum of vaccum [sic] energy of the binding molecule and
nonbond energy between the binding molecule and the target
molecule; polar interaction energy, which is the polar component
of the total interaction energy; and phobic interaction energy,
which is the hydrophobic component of the total interaction
energy. Nonbond energy refers to the sum of Coulomb, van der
Waals, and hydrogen-bond energies.
Spec. 147.
The Examiner found that Cho describes the same steps of claim 1 of
providing molecular poses and clustering the poses into families. Final Act.
8. The Examiner found that Cho teaches calculations of A) total interaction
energy, but not selecting poses based on the individual energy components
as in the claim, i.e., B) and C). Id. at 9. However, the Examiner found it
would have been obvious to have selected poses based on the interaction
energy of interest. As evidence, the Examiner cited the Itai and McConkey
publications describing hydrogen bonding, van der Waals, electrostatic, and
hydrophobic interactions as important interactions in stable binding between
ligands and target molecules and to create scoring functions. Id.
Appellants contend that there is no teaching or suggestion in the cited
publications to perform all three selections (A, B, and C above) to select
molecular poses. Appeal Br. 22.
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Findings of Fact (“FF”)
We begin with the most pertinent facts.
Cho Publication
Cho discloses:
To help improve the accuracy of protein-ligand docking
as a useful tool for drug discovery, we developed MPSim-Dock,
which ensures a comprehensive sampling of diverse families of
ligand conformations in the binding region followed by an
enrichment of the good energy scorin g families so that the energy
scores of the sampled conformations can be reliably used to
select the best conformation of the ligand.
Cho, Abstract.
FF2.
We used the Dreiding all-atom FF for both the protein and
the ligand. This includes the internal energy of the ligand along
with the nonbond energy of interaction with the protein. The
energy expression includes valence energies (bonds, angles,
torsion, and inversion) and nonbond interactions (Coulomb, van
der Waals, and hydrogen bond) within the ligand and with the
protein.
Id. at 49 (footnote omitted).
Itai discloses:
Itai Publication
FF3.
It is known from the crystallographic analyses of biopolymer-
ligand molecule complexes that among these intermolecular
interactions, hydrogen-bond, electrostatic and hydrophobic
interactions and the like are particularly important. In drug
design and structure-activity relationship study, it is very
important to know whether a compound molecule can form a
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stable complex with its target biopolymer and, if so, what kind
of binding mode the complex has (i.e., which functional group in
the ligand-binding site of the biopolymer interact which
functional groups in the ligand molecule in what kind of mode)
and how stable the complex is.
Itai 14.
FF4.
F. Jiang et al. developed an automatic docking method in
which intermolecular interactions such as hydrogen-bond,
electrostatic interaction and the like are considered qualitatively
in addition to the shape complementarity which Kuntz et al.
highlighted (F. Jiang and S. Kim, J. Mol. Biol. 219, 79 (1991)).
Id. 110.
FF5.
As a result of various studies, the inventors developed
methods for docking automatically any ligand molecules to the
ligand-binding sites in biopolymers by searching the binding
modes of stable complexes and the active conformations of the
ligand molecules at the same time by taking into account
hydrogen-bond, electrostatic interaction and van der Waals force
as the interactions between the biopolymers and the ligand
molecules, and they succeeded in solving the above-mentioned
problems.
Id. 114.
FF6.
Thus, all possible combinations of the hydrogen-bonds formed
by the biopolymer and ligand molecule are selected and thereby
the mode of binding of the ligand molecule to the biopolymer
can be searched systematically and efficiently.
Id. 174.
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FF7.
The intermolecular interaction energy between the
biopolymer and the hydrogen-bonding part of the ligand
molecule (Einter) can be calculated by the following formula:
F- =
where Gvdw (k) is the van der Waals interaction energy of atom
k, Geic (k) is the electrostatic interaction energy of atom k and qk
is the atomic charge on atom k.
Id. 199
McConkey Publication
McConkey discloses:
FF8.
The most common means of estimating a binding affinity
to be used as a scoring function is by partitioning of the free
energy into recognizable components. The number and type of
terms vary between scoring functions, but in general there are
terms for hydrogen bonding, van der Waals, electrostatic and
hydrophobic interactions, and entropy penalties.
McConkey 847.
FF9.
“The weighting of each of the interaction terms is estimated by fitting
a regression model to a test set of ligand-protein complexes with known
binding affinities.” Id. at 848.
FF10.
The scoring function in GOLD is an energy partition function,
with terms for hydrogen bonding, ligand-protein interactions and
the internal energy of the ligand. Multiple atom types were used
to calculate hydrogen bond energies between donor and acceptor
pairs. . . . The internal energy of the ligand was calculated using
a 6-12 van der Waals potential and the Tripos force field. The
scoring function accounts for the desolvation of polar residues,
but does not address desolvation or lipophilic interactions
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explicitly. It was effective in identifying a top-ranked solution
o
within 2 A RMSD in approximately half the cases. After
publication of the validation paper, recognition of hydrophobic-
hydrophobic interactions was added to the algorithm and tested
on an additional 34 ligands, and the data were published on the
GOLD website.
Id. at 851—852 (footnote omitted).
FF11.
“There are inherent limits to some scoring approaches when used
independently of other methods. The Poisson-Boltzmann equation, for
example, can provide an accurate description of the electrostatic field around
a protein, but if used alone does not account for desolvation or other
interactions.” Id. at 855.
FF12.
“Subtle changes in electrostatic properties can result in large changes
in binding affinity within a given type of interaction. A scoring function that
is a sum of pairwise additive terms also neglects non-additive behaviour
between and among groups. Hydrophobic interactions are a good example of
this.” Id.
Discussion
Appellants’ principal argument is that the claims are nonobvious in
view of Cho, Itai, and McConkey because one of ordinary skill in the art
would not have selected molecular poses for total-, polar-, phobic interaction
energies individually, but rather would have utilized an energy scoring
function that contain these as multiple terms for one calculation of total
interaction energy. Appeal Br. 21—22. Appellants contend that the prior art
teaches away from the claimed features because the prior art teaches
utilizing all binding energies to determine the optimal binding poses. Reply
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Br. 6. Appellants also argue that Itai teaches away utilizing phobic energy
interactions for pose selections because, while Itai mentions phobic
interactions in its Background section, Itai does not use the term in its actual
calculations. Appeal Br. 21.
Appellants’ arguments do not persuade us that the Examiner erred in
determining that the claims are obvious in view of Cho, Itai, and McConkey.
The first pose selection criteria recited in the claim is selecting poses
based on “total interaction energy.” The definition in the Specification of
“total interaction energy” includes Coulomb, van der Waals, hydrogen-bond
energies, and hydrophobic energies. Spec. 147. These energy components
appear to be the same energy components described in Cho (FF2), Itai (FF3,
FF4, FF5), and McConkey (FF8, FF10) for determining total interaction
action for selecting binding molecule poses. Thus, the first selection criteria
recited in claim 1 used to select molecular poses is disclosed in or suggested
by the teachings in Cho, Itai, and McConkey, which teach that total
interaction energy is important in determining the binding between binding
and target molecules.
The second and third pose selection criteria recited in the claim use
polar and phobic energy interactions, respectively, to select binding poses.
Appellants contend that one of ordinary skill in would not have used these
criteria individually to select molecular poses.
We agree with the Examiner that there would have been reason to
select poses based on polar and phobic energy interactions, individually.
The cited publications indicate that the persons of skill in the art were
developing methods to improve energy scoring and identify parameters to
improve it. FF1, FF3, FF4, FF5, FF10, FF11. One of ordinary skill in the
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art who wanted to improve energy scoring for the purpose of modeling
interactions between a binding molecule and its target would have sought to
understand the individual contributions by each energy component when
determining what poses to select.
For example, Itai describes prior docking programs in its background
section. FF4. Itai characterizes its method as an improvement over the prior
art by “taking into account hydrogen-bond, electrostatic interaction and van
der Waals force as the interactions between the biopolymers and the ligand
molecules.” FF5. McConkey describes utilizing the GOLD energy scoring
function that takes into account hydrogen bonding and van der Waals forces.
FF10. McConkey teaches that the scoring function was subsequently
improved by adding hydrophobic interactions to the scoring function. FF10.
McConkey also acknowledges limitations to current scoring approaches.
FF11. Thus, both publications indicate that the ordinary skilled worker
sought to adjust the energy scoring function by adding energy interaction
terms to improve its ability to pick the best poses between the binding and
target molecules.
Itai also teaches selecting “all possible combinations of the hydrogen-
bonds formed by the biopolymer and ligand molecule” to search for the
mode of binding (FF6), providing a further reason to determine how
hydrogen bonding (a polar bond energy interaction B as in the claims)
influences the selection of binding poses.
McConkey teaches “estimating a binding affinity to be used as a
scoring function ... by partitioning of the free energy into recognizable
components” (FF8) and weighting each of the interaction terms (FF9), thus
also prompting one of ordinary skill in the art to look at the contribution of
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the individual recognizable energy component when selecting molecular
poses. McConkey further states that “[sjubtle changes in electrostatic
properties can result in large changes in binding affinity within a given type
of interaction” (FF12), again providing the ordinary skilled worker with
reason to evaluate the effect of individual energy interactions on binding
poses.
Thus, based on these teachings, one of ordinary skill in the art, would
have had reason to determine the individual energy contributions to the total
interaction energy to determine how effective they are alone, and in
combination with other energy interaction components, in selecting
molecular poses.
For the foregoing reasons, Rejection 1 of claim 1 is affirmed. The
same arguments were made for claim 21. Appeal Br. 19. Thus, the rejection
of claim 21 is affirmed for the same reasons. Because separate arguments
were not provided for claims 2—5, 8—10, 18, 19, and 21—23 (Rejection 1) and
claims 11—20 (Rejection 2) {Id. at 23, 24), those claims fall with claims 1
and 21. 37 C.F.R. § 41.37(c)(l)(iv).
SECTION 101 REJECTION
The Examiner rejected the claims as directed to a judicial exception to
patent eligibility under 35 U.S.C. § 101. Final Act. 2—3. The Examiner
found that the claims are directed to an abstract idea performed on a
computer to predict binding poses of a molecule to a target molecule, such
as a receptor. Id. at 4. The Examiner stated the claimed steps are directed to
“to data manipulation, which is an abstract construct, having no particular
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concrete or tangible form” which do not add significantly more to the idea,
itself. Id. at 5.
Appellants contend that the claims “are not dealing with something as
abstract as ‘economic value’, nor are they dealing with claiming
mathematical formulas or algorithms regarding numbers just as numbers in
and of themselves — the algorithms of the instant claims are procedural
method steps dealing with numbers representative of physical properties of
objects (molecules).” Appeal Br. 10. Appellants contend that the steps are
not “just ‘data manipulation’” but can be used for rational drug design.” Id.
at 10-11. Appellants also state “that, seen as a whole, the claims present
something significantly more than an abstract idea due to the claim’s
relationship to a technological art.” Id. at 15. Appellants also contend that
the claims “are not merely implementing conventional steps for ‘predicting
binding poses of a molecule binding to its receptor.’” Id. at 14.
Specifically, Appellants contend that selecting molecular poses based on
total interaction energy, polar interaction energy, and phobic interactions is
not conventional. Id.
Discussion
The determination of patent eligibility under 35 U.S.C. § 101 is a
two-step analysis. First, it must be determined whether the claims are
directed to patent-ineligible concept, e.g., a law of nature, natural
phenomenon, or abstract idea. Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 134
S. Ct. 2347, 2355 (2014). Second, the elements of the claims, “both
individually and as an ordered combination,” are considered “to determine
whether the additional elements transform the nature of the claim into a
patent-eligible application of that abstract idea.” DDR Holdings, LLC v.
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Hotels.com, L.P., 773 F.3d 1245, 1255 (2014). “This second step is the
search for an ‘inventive concept,’ or some element or combination of
elements sufficient to ensure that the claim in practice amounts to
‘significantly more’ than a patent on an ineligible concept.” Id. (quoting
Alice, 134 S. Ct. at 2347).
The Federal Circuit acknowledges that it is difficult to discern when
claims are directed to an abstract idea. DDR Holdings, 773 F.3d at 1255.
Because of this difficulty, the courts have taken a case-by-case approach:
“Instead of a definition, then, the decisional mechanism courts now apply is
to examine earlier cases in which a similar or parallel descriptive nature can
be seen—what prior cases were about, and which way they were decided.”
Amdocs (Israel) Limited v. Openet Telecom, Inc., 841 F.3d 1288, 1294
(2016). In other words, the courts look to the similarities and differences
with other claims subject to a patent eligibility analysis in earlier decided
cases to determine whether the claims at issue are directed to subject matter
eligible for a patent.
We thus must first decide whether the claim is directed to patent-
ineligible subject matter. We begin with the purpose of claim 1.
Claim 1 is a “computer operated method for predicting binding poses
of a binding molecule.” The Specification teaches that the process can be
used in rational drug design to design a drug to bind to a target molecule,
such as a protein. Spec. H 3, 7.
The claim begins with a step of providing at least one molecule pose
for the binding molecule. As explained in the Specification, a molecular
pose is conformation of a molecule, i.e., a shape or configuration of it in
space. Id. Tflf 3, 32. The claim does not recite how the poses are determined,
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but the Specification explains that poses can be generated utilizing a
program, such as MacroModel. Id. 29, 30. Thus, a known algorithm can
be used to produce the molecular poses.
The poses are clustered into families, “where a family is a group of
molecular poses in the population of molecular poses that show similar
positions (also known as orientations) with respect to the target molecule.”
Id. 134. The claims do not recite how the clustering is performed.
However, the Specification teaches that “clustering (S 110) into families is
based on RMSD (root mean square difference) calculations between any two
molecular poses. Specifically, distance between two molecular poses is
calculated by averaging deviation of the two poses over all heavy (non­
hydrogen) atoms.” Id. 136. Thus, clustering can be performed using a
mathematical formula.
The claim further recites that molecular poses from the families are
selected based on interaction energy between the pose and the target
molecule. As discussed above, the selecting step is performed based on
total-, polar-, and phobic interaction energies. Neither the claims nor the
Specification explain how the interaction energy calculations are
accomplished. Thus, any conventional way of calculating energies can be
used. The Specification teaches that the interaction energies are used to pick
the “best” binding poses. Id. 144.
In sum, all the recited steps in the claim utilize algorithms in
determining poses, family clusters, and interaction energies. For this reason,
we agree with the Examiner that the claims are directed to “data
manipulation,” where the data is the computer representations of the poses,
clusters, and energies that are manipulated to select the best molecular poses.
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We thus turn to the recent cases to determine whether the claimed subject
matter is eligible for a patent under § 101.
In Digitech Image Technologies, LLC v. Electronics for Imaging, Inc.,
758 F.3d 1344, 1348 (2014), the claims were directed to “a process of taking
two data sets and combining them into a single data set, the device profile.
The two data sets are generated by taking existing information—i.e.,
measured chromatic stimuli, spatial stimuli, and device response
characteristic functions—and organizing this information into a new form.”
The court found that the method claims were drawn to “an abstract idea
because it describes a process of organizing information through
mathematical correlations and is not tied to a specific structure or machine.”
Digitech, 758 F.3d at 1350, Furthermore, the court held:
The above claim thus recites an ineligible abstract process of
gathering and combining data that does not require input from a
physical device. As discussed above, the two data sets and the
resulting device profile are ineligible subject matter. Without
additional limitations, a process that employs mathematical
algorithms to manipulate existing information to generate
additional information is not patent eligible.
Id. at 1351.
The claims in this case are similar to Digitech because, while the
algorithms to determine poses are performed on a computer using software,
there is no input of data from a physical device, but rather the claim appears
to solely involve the manipulation of data, beginning from data provided by
a known computer program (MacroModel, Spec. ®jff[ 29, 30) that generates
molecular poses.
The claims in this case are distinguishable from McRO, Inc. v. Bandai
Namco Games Am. Inc., 837 F.3d 1299, 1313 (Fed. Cir. 2016), which
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involved computer automation “to produce accurate and realistic lip
synchronization and facial expressions in animated characters” that
previously could only be produced by human animators.” In McRO, while
the claims involved the manipulation of data, e.g., generating morph weight
sets to animate lip and facial expressions of three dimensional characters, the
court found that “the automation goes beyond merely ‘organizing [existing]
information into a new form’ [as in Digitech] or carrying out a fundamental
economic practice.” McRO, 837 F.3d at 1315. Instead, the court found that
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: a sequence of synchronized, animated characters.” Id.
The rejected claims in this case are different because the data is not
used to produce a new result, such as the animation of characters in McRO,
but rather the data is used to select poses from a family of clustered poses
which are generated by a known and conventional software program. In
fact, the claim does not require that even the best poses are selected nor does
the claim require the selected poses to be utilized in anyway.
The claims are also different from the claims in Diamond v. Diehr,
450 U.S. 175 (1981) (“Diehr”) which were found to be patent eligible. In
Diehr, the claims were directed to a method of operating a rubber-molding
press of precision molded compounds. Id. at 179, fn. 5 (reproducing claims
1,2, and 11). The temperature in the mold during the rubber-molding
process was constantly determined and provided to a digital computer. Id.
The computer calculated the Arrhenius equation for the reaction time during
the cure using the temperature and used the equation to determine when to
open the press. Id.
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Although the claim recited a mathematical algorithm, namely the
Arrhenius equation, the Court held that the claim was eligible for a patent.
[W]hen a claim containing a mathematical formula implements
or applies that formula in a structure or process which, when
considered as a whole, is performing a function which the patent
laws were designed to protect (e. g., transforming or reducing an
article to a different state or thing), then the claim satisfies the
requirements of § 101
Diehr, 450 U.S. at 192. The Court emphasized that the process in Diehr was
to make rubber, and the mathematical formula was simply used to determine
when to open the mold so over curing did not occur. Id. at 1057. In this
case, the claimed steps of providing poses, clustering, and selecting based on
interaction energies do not involve a change in how the process is carried as
it did in Diehr (i.e., opening the mold). The steps enable poses to be
selected, but there is no requirement in the claim that selected poses are used
for a particular purpose or even that the best poses are selected. Indeed, it is
not even clear whether poses based on only phobic or polar interaction
energies would be better than poses based on total interaction energy as
required by the claims. The claim merely selects poses based on phobic and
polar interaction energies, but does not contain a step in which these poses
are used or combined with the total interaction energy. Rather, the steps
involve merely the collection of data without any application of it.
The claims are also not directed to an improvement in computer
functionality as in Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1335—36
(Fed. Cir. 2016), where a basis for patent eligibility was found.
In sum, we conclude that the claims are directed to a patent ineligible
concept.
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While we agree with the Examiner that the claim is directed to an
abstract idea, we further note that the claim is also directed to an ineligible
natural law or phenomenon because it merely informs the relevant audience
of the factors that affect the molecular poses between a naturally-occurring
binding molecule and target, namely factors that affect the native
conformation of a ligand or substrate bound to naturally occurring protein.
See, e.g., Itai ^ffj 121, 122, 127, 137 (Example 2) (describing the binding
mode of naturally-occurring dihydrofolate reductase and its substrate). As
held in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 132
S .Ct. 1289, 1297 (2012), a patent which simply describes a relation that
“exists in principle apart from any human action,” namely, the binding
between a naturally-occurring protein and its ligand or substrate, is a natural
law and patent ineligible subject matter. Consistently, Appellants
characterize the claims as “representative of physical properties of objects
(molecules).” Appeal Br. 10. The properties of a molecule are naturally-
occurring and thus encompass a natural phenomenon, falling within the
judicial exception to patent eligibility.
Appellants contend that the claims are more than just “data
manipulation” because they simulate physical systems. Appeal Br. 9.
However, simply because the data is a representation of a physical molecule
does not exclude it from being an abstract idea because none of the steps are
tied to the physical molecule, itself, or interact in any way with the physical
molecule or a process of manipulating it.
The second step of the patent eligibility analysis requires a
determination of whether the claims do significantly more than simply
describe the abstract idea or natural law. Mayo, 132 S. Ct. at 1297. The
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Application 12/944,700
claim limitations must be scrutinized to determine whether the claims
contain an “inventive concept” to “transform” the claim into patent-eligible
subject matter. Alice, 134 S. Ct. at 2357 (quoting Mayo, 132 S. Ct. at 1298).
The transformation of an abstract idea into patent-eligible subject
matter “requires more than simply stat[ing] the [abstract idea]
while adding the words ‘apply it.’” Id. (quoting Mayo, 132 S.Ct.
at 1294) (alterations in original). “A claim that recites an abstract
idea must include ‘additional feature’ to ensure ‘that the [claim]
is more than a drafting effort designed to monopolize the
[abstract idea].”’ Id. (quoting Mayo, 132 S.Ct. at 1297)
(alterations in original). Those “additional features” must be
more than “well-understood, routine, conventional activity.”
Mayo, 132 S. Ct. at 1298.
Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 715 (Fed. Cir. 2014).
As discussed in connection with the rejection based on obviousness,
the steps of providing molecular poses, clustering the poses into families,
and utilizing total energy interactions to select poses was “well-understood,
routine, conventional activity” as established by the teachings of Cho relied
upon by the Examiner in the obviousness rejection. Final Act. 6—7. The
additional steps of selecting poses individually based only on polar and
phobic interactions involve the same conventional step of selecting energy
interactions as described in Cho, Itai, and McConkey. We fail to see any
technical improvement embodied by the claim, particularly when it was
known in the prior art to select poses based on total interaction energy.
Appellants did not provide evidence that such selection steps based on polar
and phobic energy interactions alone provided better pose selection or
operate in an unconventional manner. Amdocs, 841 F.3d at 1300-01.
Appellants also contend that the claims do not preempt an abstract
idea. Appeal Br. 12. However, as discussed in Ariosa Diagnostics, Inc. v.
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Application 12/944,700
Sequenom, Inc., 788 F.3d 1371 (2015), 1379, “[wjhile preemption may
signal patent ineligible subject matter, the absence of complete preemption
does not demonstrate patent eligibility.” Moreover, Ariosa held: “Where a
patent’s claims are deemed only to disclose patent ineligible subject matter
under the Mayo framework, as they are in this case, preemption concerns are
fully addressed and made moot.” Consequently, since the claimed subject
matter is ineligible under Mayo, we need not address the preemption
concern.
SUMMARY
For the foregoing reasons, the obviousness rejections (Rejections 1
and 2), and the 101 rejection (Rejection 3) are affirmed.
TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l)(iv).
AFFIRMED
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