Ex Parte Ahuja et al

Patent Trial and Appeal Board

Dec 3, 2014

10966041 (P.T.A.B. Dec. 3, 2014)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte SACHIN AHUJA, DAVID KITA,
ENIKO FODOR, and ADITYO PRAKASH
__________

Appeal 2012-007002
Application 10/966,041
Technology Center 1600
__________

Before ERIC B. GRIMES, JEFFREY N. FREDMAN, and
ULRIKE W. JENKS, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to a method
for determining whether a biomolecule is a lead candidate for a target. The
Examiner rejected the claims as failing to comply with the written
description requirement and as obvious. We have jurisdiction under
35 U.S.C. § 6(b). We reverse.

1 Appellants identify the Real Party in Interest as the Verseon
Corporation (see App. Br. 3).
Appeal 2012-007002
Application 10/966,041

2
Statement of the Case
Background
“Rational drug design generally uses structural information about drug
targets (structure-based) and/or their natural ligands (ligand-based) as a basis
for the design of effective lead candidate generation and optimization”
(Spec. 3, ll. 27–29). The Specification teaches that the “use of
computational modeling in the context of rational drug design has been
largely motivated by a desire to both reduce the required time and to
improve the focus and efficiency of drug research and development, by
avoiding often time consuming and costly efforts in biological ‘wet’ lab
testing” (Spec. 4, ll. 10–13).
“This invention is generally concerned with providing a method to
generate molecular representations in a manner to enable efficient molecular
processing in a variety of scenarios” (Spec. 7, ll. 3–4).
The Claims
Claims 1–15, 17–27, 29–39, 41–48, 50–55, 57, 58, and 60–64 are on
appeal. Independent claim 1 is representative and reads as follows:
1. A method for determining whether a biomolecule is a
lead candidate for a target, the method comprising:
receiving, at a partitioning engine of a circuit, a
molecular representation of a molecular subset of the
biomolecule or the target or both, the molecular subset
comprising a plurality of atoms and bonds;
receiving, at the partitioning engine, a set of molecular
transformations for all or at least one part of the molecular
representation, wherein the set of molecular transformations
includes at least one rotation operator;
receiving, at the partitioning engine, a set of partitioning
operators and a set of partitioning criteria, wherein the
Appeal 2012-007002
Application 10/966,041

3
partitioning criteria includes a maximum size of a storage unit
of the circuit;
partitioning, with the partitioning engine, the molecular
representation into a plurality of resultant subrepresentations,
wherein the partitioning depends on the set of molecular
transformations, the set of partitioning operators, the set of
partitioning criteria, and the maximum size of each of a
plurality of storage units of the circuit, and wherein the
partitioning is further based on an amount of unused storage
space for storing each subrepresentation into a respective
storage unit; and
determining a binding affinity between at least part of the
biomolecule and at least part of the target, wherein determining
the binding affinity includes performing a calculation involving
the molecular subset, wherein the calculation includes
computing molecular transformations for respective resultant
subrepresentations, and wherein the binding affinity is used to
determine whether the biomolecule is a lead candidate.

The issues
A. The Examiner rejected claim 62 under 35 U.S.C. § 112, first
paragraph, as failing to comply with the written description requirement
(Ans. 6–7).
B. The Examiner rejected claims 1–3, 5, 21–26, 29–32, 39, 41–43, 47,
48, 50, 51, 54, 55, and 61–64 under 35 U.S.C. § 103(a) as obvious over
Ewing2 and Rohwer3 (Ans. 7–13).
C. The Examiner rejected claim 4 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Cho4 (Ans. 13–14).

2 Ewing et al., DOCK 4.0: Search strategies for automated molecular
docking of flexible molecule databases, 15 J. COMPUTER-AIDED MOLECULAR
DESIGN 411-428 (2001).
3 Rohwer, T. A., US 5,241,663, issued Aug. 31, 1993.
Appeal 2012-007002
Application 10/966,041

4
D. The Examiner rejected claims 6–8 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Brooks5 (Ans. 15).
E. The Examiner rejected claim 9 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Smith6 (Ans. 16–17).
F. The Examiner rejected claims 10 and 11 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, and Rarey7 (Ans. 17–18).
G. The Examiner rejected claim 60 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Klinger8 (Ans. 18–19).
H. The Examiner rejected claims 12, 17–20, 52, and 53 under 35 U.S.C.
§ 103(a) as being obvious over Ewing, Rohwer, and Lewell9 (Ans. 20-22).
I. The Examiner rejected claims 13–15 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, Lewell, and Wise10 (Ans. 22–24).

4 Cho et al., Binary Formal Inference-Based Recursive Modeling Using
Multiple Atom and Physicochemical Property Class Pair and Torsion
Descriptors as Decision Criteria, 40 J. CHEM. INF. COMPUT. SCI. 668–680
(2000).
5 Brooks et al., CHARMM: A Program for Macromolecular Energy,
Minimization, and Dynamics Calculations, 4 J. COMPUTATIONAL CHEMISTRY
187–217 (1983).
6 Smith, T.J., MolView: A program for analyzing and displaying atomic
structures on the Macintosh personal computer, 13 J. MOLECULAR
GRAPHICS 122–125 (1995).
7 Rarey et al., Feature trees: A new molecular similarity measure based on
tree matching, 12 J. COMPUTER-AIDED MOLECULAR DESIGN 471–490
(1998).
8 Klinger, V., DiPaCS A New Concept for Parallel Circuit Simulation, IEEE
SIMULATION SYMPOSIUM 32–41 (1995).
9 Lewell et al., RECAP-Retrosynthetic Combinatorial Analysis Procedure: A
Powerful New Technique for Identifying Privileged Molecular Fragments
with Useful Applications in Combinatorial Chemistry, 38 J. CHEM. INF.
COMPUT. SCI. 511–522 (1998).
Appeal 2012-007002
Application 10/966,041

5
J. The Examiner rejected claims 33–38, 44–46, 57, and 58 under 35
U.S.C. § 103(a) as being obvious over Ewing, Rohwer, Parks,11 and
Koubogiannis12 (Ans. 24–32).
K. The Examiner rejected claim 27 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Schneider13 (Ans. 32–33).
A. 35 U.S.C. § 112, first paragraph, written description
The Examiner finds that while “passages from the specification teach
that the size of the storage unit is a constraint for partitioning, none of these
passages teach the converse- that unused storage is minimized in a way that
attempts to satisfy all of the partitioning criteria” (Ans. 7). The Examiner
finds that because “these passages for the specification are closest to the
limitations of claim 62 but do not provide support for the newly claimed
limitations and since the remaining portions of the disclosure are silent with
regard to support to this amended limitation; claim 62 is interpreted to
encompass NEW MATTER” (Ans. 7).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s finding that the Specification fails to provide
descriptive support for claim 62?

10 Wise et al., Peptide-mass fingerprinting and the ideal covering set for
protein characterization, 18 ELECTROPHORESIS 1399-1409 (1997).
11 Parks, T. J., US 5,404,454, issued Apr. 4, 1995.
12 Koubogiannis et al., Solution of flow problems using unstructured grids on
distributed memory platforms, 160 COMPUT. METHODS APPL. MECH. ENGRG.
89–100 (1998).
13 Schneider et al., Matrix-assisted Laser Desorption Mass
Spectrometry of Homopolymer Oligodeoxyribonucleotides. Influence of Base
Composition on the Mass Spectrometric Response, 28 ORGANIC MASS
SPECTROMETRY 1353–1361 (1993).
Appeal 2012-007002
Application 10/966,041

6
Findings of Fact
1. Claim 62 recites: “The method of claim 32, wherein the
minimization of the total amount of unused storage for storing the plurality
of subrepresentations in the plurality of storage units is performed as part of
an attempt to satisfy all of the partitioning criteria.”
2. The Specification teaches that “if any subgraphs still need
further partitioning, all types of links, not just invariant links, can be
removed, and nodes can be cleaved until the resulting subgraphs satisfy a
final set of criteria” (Spec. 11, ll. 11–13).
3. The Specification teaches that:
The size of a representation storage unit can be used as a
constraint on partitioning. For example, if a subrepresentation
needs more storage than a representation storage unit, then it is
partitioned further. In another example, partitioning may be so
constrained such that the total amount of unused storage,
summed for all representation storage units in use, is
minimized.

(Spec. 39, ll. 8–12).
Analysis
The Examiner finds that although the “passages from the specification
teach that the size of the storage unit is a constraint for partitioning, none of
these passages teach the converse - that unused storage is minimized in a
way that attempts to satisfy all of the partitioning criteria” (Ans. 7).
Appellants contend that “the Examiner believes that somehow this
description states that there is other criteria that are not satisfied. But, such
an interpretation contradicts the use of ‘until’” (Reply Br. 2). Appellants
contend that the “nodes are cleaved until the final set of criteria is satisfied.
Appeal 2012-007002
Application 10/966,041

7
If certain criteria are not satisfied, then such criteria would not be part of the
set that is being used, since the nodes are cleaved until the set of criteria is
satisfied” (Reply Br. 2).
We find that Appellants have the better position. We agree that
Appellants’ interpretation of the phrase “until the resulting subgraphs satisfy
a final set of criteria” in the Specification as describing “all of the
partitioning criteria” required by claim 62 is reasonable.
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that the Specification fails to provide descriptive support for claim 62.
B. 35 U.S.C. § 103(a) over Ewing and Rohwer
The Examiner finds that Ewing teaches “the docking program DOCK
4.0 and search strategies for automated molecular docking of flexible
molecule databases” (Ans. 9). The Examiner finds that Ewing’s search
strategies include “partitioning based on partitioning operators wherein the
criteria include partitioning at the rotatable bonds” (Ans. 9).
The Examiner acknowledges that Ewing “does not teach that the
criterion of partitioning includes the maximum size of each of the plurality
of storage units of the circuit. Additionally, Ewing et al. does not require
that this partitioning is further based on an amount of unused storage space
for storing each subrepresentation into a respective storage unit” (Ans. 9–
10).
The Examiner finds that Rohwer teaches that “video data is divided
among the storage units such that the amount of unused storage is
minimized. Consequently, this video data is partitioned in a way that both
Appeal 2012-007002
Application 10/966,041

8
takes into account maximum storage of each storage unit and minimized
unused storage” (Ans. 10).
The Examiner finds it obvious to
modify the computational partitioning and transformation
studies of Ewing et al. by use of the computer storage methods
of video files of Rohwer wherein the motivation would have
been that partitioning data based on size such that unused
storage is minimized (as in Rohwer) is performed in a way that
increases efficiency of storage by minimizing the amount of
wasted storage

(Ans. 13).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that Ewing and Rohwer render the claims
obvious?
Findings of Fact
4. Ewing teaches molecular docking, which requires “finding the
low-energy binding modes of a small molecule, or ligand, within the active
site of a macromolecule, or receptor, whose structure is known. Solving the
docking problem computationally requires an accurate representation of the
molecular energetics as well as an efficient algorithm to search the potential
binding modes” (Ewing 411, col. 1).
Appeal 2012-007002
Application 10/966,041

9
5. Figure 2 of Ewing is reproduced below:

Figure 2 describes a process where “[b]ased on the location of rotatable
bonds, the molecule is then divided into rigid, overlapping segments
(Figure 2B)” (Ewing 412, col. 2).
Appeal 2012-007002
Application 10/966,041

10
6. Figure 4 of Rohwer is reproduced below:

Referring to FIG. 4, the first subroutine 1000 determines the
number of and data storage capacities of the memory CCAs 18.
The first step 1002 is to initialize some program constants. The
maximum number BM of boards, i.e., memory CCAs 18, is
initialized at four and the maximum number FM of frames is
initialized at 128. A loop counter C is initialized at zero and a
board count variable BC is initialized at zero.

(Rohwer, col. 12, ll. 30–37).

Appeal 2012-007002
Application 10/966,041

11
7. Rohwer teaches that
numerous permutations of possible data storage capacities exist
among the four memory CCAs 18. However, by programming
the memory and system controller 16 to begin with the largest
capacity memory CCA 18 and pairing it, or portions thereof, in
overlapped pairings with successively smaller capacity memory
CCAs 18, or alternatively, pairing the memory CCAs 18 in
staggered overlapped pairings, efficient pairings of data storage
capacities are accomplished, while supporting the simultaneous
video data write and read operations and minimizing the
amount of unused, and therefore wasted, video data storage
capacity.

(Rohwer, col. 11, l. 66 to col. 12, l. 9).
8. Rohwer teaches that “[w]ith a maximum frame capacity of 32
frames per memory CCA 18 in the preferred embodiment, the maximum
frame storage capacity is 128 frames. Therefore, in such a preferred
embodiment, the maximum number BM of boards is four and the maximum
number of frames FM is 128” (Rohwer, col. 12, ll. 41–46).
Principles of Law
“A reference is reasonably pertinent if, even though it may be in a
different field from that of the inventor’s endeavor, it is one which, because
of the matter with which it deals, logically would have commended itself to
an inventor’s attention in considering his problem.” In re Clay, 966 F.2d
656, 659 (Fed. Cir. 1992).
Analysis
Appellants contend that
Rowher is not reasonably pertinent to the particular problem of
the claimed invention. Rowher is directed to the problem of
storing and reading video images at the same time so that two
Appeal 2012-007002
Application 10/966,041

12
video images can be displayed. Rowher’s solution is to store
each video frame in a particular location of memory . . . so that
more frames may be stored. The claimed invention is not
related to being able to store more data, nor is the claimed
invention related to the problem of having to store and read data
at the same time.

(App. Br. 11).
The Examiner finds that “both Ewing et al. and Rohwer pertain to the
same problem. Specifically, since Ewing pertains to searching and storing
biophysical data and Rohwer pertains to searching and storing image/video
data, both Ewing et al. and Rohwer pertain to the analogous problem of data
storage, data searching, and data manipulation” (Ans. 35).
We find that Appellants have the better position. Rohwer is plainly
directed towards a different field of endeavor than Ewing. Therefore, the
issue is whether the teachings of Rohwer are reasonably pertinent to the
molecular docking process of Ewing. In particular, the analogous art test
asks whether the ordinary artisan, intent on improving the molecular docking
process of Ewing, would have reasonably looked to the data storage methods
of Rohwer.
Rohwer relies upon general data storage and processing methods for
“supporting the simultaneous video data write and read operations and
minimizing the amount of unused, and therefore wasted, video data storage
capacity” (Rohwer, col. 12, ll. 7–9; FF 7). Such a problem is not reasonably
pertinent to the particular problem with which Ewing was involved,
segmenting molecules based on the location of the rotatable bonds, in order
to define anchor segments which may be used for automated molecular
docking to identify interacting compounds of interest (FF 4–5).
Appeal 2012-007002
Application 10/966,041

13
The Examiner’s attempt to frame Ewing as teaching a method which
generally analyzes biophysical data and Rohwer as teaching a method of
efficiently storing, searching, and manipulating data (see Ans. 35) is
unreasonably broad, and fails to provide any specific connection between the
two methods. This is dramatically different than situations where the
analogous art test was satisified, such as the Federal Circuit’s decision in
Icon, where the reference and the invention both dealt with a much more
narrowly framed issue of substituting different types of hinges. See In re
Icon Health and Fitness, Inc., 496 F.3d 1374, 1380 (Fed. Cir. 2007).
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that Ewing and Rohwer render the claims obvious.
C-K. 35 U.S.C. § 103(a) rejections
These rejections rely upon the underlying obviousness rejection over
Ewing and Rohwer. Having reversed the rejection of claim 1, we also
necessarily reverse these obviousness rejections because the Examiner does
not rely upon any of the remaining prior art to address the partitioning
limitation of claim 1.
SUMMARY
In summary, we reverse the rejection of claim 62 under 35 U.S.C.
§ 112, first paragraph, as failing to comply with the written description
requirement.
We reverse the rejection of claims 1–3, 5, 21–26, 29–32, 39, 41–43,
47, 48, 50, 51, 54, 55, and 61–64 under 35 U.S.C. § 103(a) as obvious over
Ewing and Rohwer.
Appeal 2012-007002
Application 10/966,041

14
We reverse the rejection of claim 4 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Cho.
We reverse the rejection of claims 6–8 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, and Brooks.
We reverse the rejection of claim 9 under 35 U.S.C. § 103(a) as being
obvious over Ewing, Rohwer, and Smith.
We reverse the rejection of claims 10 and 11 under 35 U.S.C. § 103(a)
as being obvious over Ewing, Rohwer, and Rarey.
We reverse the rejection of claim 60 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, and Klinger.
We reverse the rejection of claims 12, 17–20, 52, and 53 under
35 U.S.C. § 103(a) as being obvious over Ewing, Rohwer, and Lewell.
We reverse the rejection of claims 13–15 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, Lewell, and Wise.
We reverse the rejection of claims 33–38, 44–46, 57, and 58 under 35
U.S.C. § 103(a) as being obvious over Ewing, Rohwer, Parks, and
Koubogiannis.
We reverse the rejection of claim 27 under 35 U.S.C. § 103(a) as
being obvious over Ewing, Rohwer, and Schneider.

REVERSED
lp