Ex Parte Friesner et al

Patent Trial and Appeal Board

Sep 6, 2018

13079489 (P.T.A.B. Sep. 6, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/079,489 04/04/2011
26161 7590 09/10/2018
FISH & RICHARDSON P.C. (BO)
P.O. BOX 1022
MINNEAPOLIS, MN 55440-1022
FIRST NAMED INVENTOR
Richard A. Friesner
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
17367-0015001 9846
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
09/10/2018 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):
P ATDOCTC@fr.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte RICHARD A. FRIESNER and ROBERT MURPHY 1
Appeal2018-005300
Application 13/079,489
Technology Center 1600
Before JEFFREY N. FREDMAN, RYAN H. FLAX, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
FLAX, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134(a) involving
claims directed to a method of scoring binding affinity of a plurality of
proposed ligand molecules for a receptor molecule using a computer and
computer databases. Claims 1 and 2 are on appeal as rejected under
35 U.S.C. § 101. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.
1 Appellants identify the Real Party in Interest as "Schrodinger, Inc."
Appeal Br. 1.
Appeal2018-005300
Application 13/079,489
STATEMENT OF THE CASE
Claims 1, the sole independent claim, is representative:
1. A method of scoring binding affinity of a plurality of proposed
ligand molecules for a receptor molecule using a computer
and computer data bases, the receptor being a protein, method
compnsmg:
a) obtaining computer stored data representing a predicted
ligand-receptor structure,
b) assigning a penalty to be added to the binding affinity
score by computerized operations which includes the
following steps:
i. determine whether a dissociated receptor of the
predicted ligand-receptor structure includes
localized solvating water molecule(s) that a) are
proximate to a formally charged group of the
receptor and b) have a larger occupancy density
at the hydration site compared to the number
density of bulk solvent, and c) form hydrogen
bonds with a charged atom of an amino acid
residue in a side chain of the receptor protein,
whereby desolvation of said localized solvating
water molecules into the surrounding
environment requires energy,
ii. determine whether the configuration of the
receptor-ligand complex requires desolvation of
one or more of the localized solvating water
molecule(s) referred to above in (i), and, if so,
iii. assign a desolvation penalty to be added to the
binding affinity score of the ligand provided,
however, that the scoring includes determining
whether a charged atom of the amino acid residue
that includes the side chain atom is in a salt bridge
with an oppositely charged receptor atom,
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Application 13/079,489
and, if so, the penalty is not assessed,
identifying one or more active complexes based on the
scored binding affinities for the plurality of proposed ligand
molecules and receptor molecule; and
testing a proposed ligand molecule of at least one of the
identified active complexes, wherein the scored binding
affinities discriminate one or more inactive complexes to
facilitate screening the plurality of proposed ligand molecules for
binding to the receptor molecule.
Appeal Br. 11-12 (Claims Appendix).
The following rejections are appealed:
Claims 1 and 2 stand rejected under 35 U.S.C. § 101 as directed to
patent-ineligible subject matter. Final Action 3.
DISCUSSION
"[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting aprimafacie case ofunpatentability. If
that burden is met, the burden of coming forward with evidence or argument
shifts to the applicant." In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992)
( emphasis added).
"Phenomena of nature, though just discovered, mental processes, and
abstract intellectual concepts are not patentable, as they are the basic tools of
scientific and technological work." Mayo Collaborative Servs. v.
Prometheus Labs, Inc., 566 U.S. 66, 71 (2012) (quoting Gottschalkv.
Benson, 409 U.S. 63, 67 (1972)). Claims directed to nothing more than
abstract ideas (such as mathematical algorithms), natural phenomena, and
laws of nature are not eligible for patent protection. Diamond v. Diehr, 450
U.S. 175, 185 (1981); accordMPEP § 2106 (II) (discussingDiehr); see also
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Application 13/079,489
Parker v. Flook, 437 U.S. 584, 592-94 (1978) (if, once the mathematical
algorithm is removed from consideration, nothing patentable remains, the
claims are not patent-eligible).
In analyzing patent-eligibility questions under 35 U.S.C. § 101, the
Supreme Court instructs us to "first determine whether the claims at issue
are directed to a patent-ineligible concept." Alice Corp. Pty. Ltd. v. CLS
Banklnt'l, 134 S. Ct. 2347, 2355 (2014). If the claims are so-directed, we
then move to a second step and "consider the elements of each claim both
individually and 'as an ordered combination' to determine whether the
additional elements 'transform the nature of the claim' into a patent-eligible
application." Id. (quoting Mayo, 566 U.S. at 78-79).
Here, under Alice's step one, the Examiner determined,
The claims are directed to a process, which is one of
statutory categories of invention. The process is a computational
method of calculating a corrected binding score of ligand-
receptor complex. The claimed invention comprises the steps of
calculating a desolvation penalty to be applied to a score
representing binding affinity of ligand to receptor. As such, the
claims are drawn to processing information, converting one form
of numerical representation into another by organizing
information through mathematical concepts, and applying rules
and categorizing information. Thus, the claims are directed to an
abstract idea which is a judicial exception.
Final Action 3. Under Alice's step two, the Examiner determined that "[t]he
claims do not include additional elements that are sufficient to amount to
significantly more than the judicial exception," noting specifically,
The claims further address a step of testing of a ligand.
The testing does not address any particular ligand, but rather -
any ligand from active ligand-receptor complexes. Further, the
"testing" is not viewed as in vitro: based on specification, the
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Application 13/079,489
"testing" is in silica testing of scoring functions. Paragraph
[058]). Even if specification had support for in vitro testing, such
testing [ for an unidentified characteristics] consist of well-
understood, routine, conventional activity of ligand testing
already engaged in by the scientific community. Essentially,
appending conventional steps, specified at a high level of
generality, to a judicial exemption, such as abstract ideas, cannot
make these ideas patent-eligible.
Id. at 3--4 (brackets in original).
It is without question that "[t]he line between a patentable 'process'
and an unpatentable 'principle' is not always clear." Flook, 437 U.S. at 589;
see also Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1150
(Fed. Cir. 2016) ("defining the precise abstract idea of patent claims in many
cases is far from a 'straightforward' exercise") (quoting DDR Holdings, LLC
v. Hotels.com, L.P., 773 F.3d 1245, 1257 (Fed. Cir. 2014)). Here, a
reasonable case could be made that the Examiner's determination under
Alice's step one is without error on the basis that the claims are directed to
the manipulation of data using mathematical algorithms. See Intellectual
Ventures I LLC v. Capital One Financial Corporation, 850 F.3d 1332,
1339--40 (2017) (claims were held to be directed to a computer programmed
to edit XML documents, which the Federal Circuit "conclude[d] [were] ...
at their core, directed to the abstract idea of collecting, displaying, and
manipulating data"); see also Electric Power Grp., LLC v. Alstom S.A., 830
F.3d 1350 (Fed. Cir. 2016). On the other hand, a reasonable case could also
be made that that the claims are not directed to a mere abstract idea, even
though they are software-based and relate to mathematical calculations,
because the claimed method solves a problem in an existing technical field
using a set of rules-based steps. See McRO, Inc. v. Bandai Namco Games
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Application 13/079,489
America Inc., 837 F.3d 1299 (Fed. Cir. 2016); see also Trading
Technologies International, Inc. v. CQG, INC, 675 Fed. Appx. 1001 (Fed.
Cir. 2017).
Even if the claims on appeal are "directed to" an abstract idea under
the first step of the Alice framework as determined by the Examiner, we
conclude that the Examiner has not established that the additional elements
recited in the claims, considered individually and as an ordered combination,
were well-understood, routine, and conventional as required under the
second step of Alice. Regarding the Examiner's determination that the non-
abstract-idea claim elements are merely routine and conventional, the
Federal Circuit has explained that
Whether something is well-understood, routine, and
conventional to a skilled artisan at the time of the patent is a
factual determination. Whether a particular technology is well-
understood, routine, and conventional goes beyond what was
simply known in the prior art. The mere fact that something is
disclosed in a piece of prior art, for example, does not mean it
was well-understood, routine, and conventional.
Berkheimer v. HP Inc., 881 F.3d 1360, 1369 (Fed. Cir. 2018).
Here, the Examiner identified that the claims require a ligand testing
step and concluded that "such testing [ for unidentified characteristics]
consist of well-understood, routine, conventional activity." Final Action 4.
However, the Examiner has identified no evidence to support this
conclusion. For this reason, we find the rejection insufficient.
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SUMMARY
The rejection of the claims as directed to patent-ineligible subject
matter is reversed.
REVERSED
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