Ex Parte Goddard et alDownload PDFPatent Trial and Appeal BoardJan 23, 201812944692 (P.T.A.B. Jan. 23, 2018) Copy Citation 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. 12/944,692 11/11/2010 William A. GODDARD III P638-US 6231 72932 7590 Steinfl + Bruno LLP 155 N. Lake Ave. Ste 700 Pasadena, CA 91101 EXAMINER BORIN, MICHAEL L ART UNIT PAPER NUMBER 1631 MAIL DATE DELIVERY MODE 01/24/2018 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, ADAM R. GRIFFITH, RAVINDER ABROL, and ISMET C. TANRIKULU1 Appeal 2016-007854 Application 12/944,692 Technology Center 1600 Before ROBERT A. POLLOCK, RYAN H. FLAX, and DAVID COTTA 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 computer-operated method for generating a second set of ligand poses based on a first set of ligand poses. Claims 5, 6, 15—17, 48, 55—58, 60, and 61 are on appeal as rejected under 35 U.S.C. §§ 101, 112, second paragraph, and 103. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 Appellants identify the Real Party in Interest as “CALIFORNIA INSTITUTE OF TECHNOLOGY.” App. Br. 2. Appeal 2016-007854 Application 12/944,692 STATEMENT OF THE CASE Claims 6, the sole independent claim, is representative: 6. A computer-operated method for generating a second set of ligand poses based on a first set of ligand poses, wherein a ligand is adapted to be bound to a receiving protein to form a ligand-protein system, the method comprising the following computer-operated steps wherein a computer performs the steps in single-processor mode or multiple-processor mode: providing the first set of ligand poses; selecting, based on user preferences, a tool of a set of tools to utilize, wherein the set of tools includes an optimization tool and an accuracy tool; wherein utilizing the optimization tool comprises performing a modification on the ligand-protein system or a portion thereof for identifying a structure associated with improved ligand-protein binding on each ligand pose in the first set of ligand poses, wherein the performing alters a structure of and optimizes a binding site of the ligand-protein system; wherein utilizing the accuracy tool comprises performing a modification on the ligand-protein system or a portion thereof for identifying a structure associated with improved ligand- protein binding on each ligand pose in the first set of ligand poses, wherein the performing improves energy calculations of the ligand-protein system; utilizing the determined tool; computing energy calculations on each ligand pose in the first set of ligand poses and the receiving protein; and generating the second set of ligand poses based on the energy calculations from the computing. App. Br. 21 (Claims App’x). 2 Appeal 2016-007854 Application 12/944,692 The following rejections are appealed: Claims 5, 6, 15—17, 48, and 55—58 stand rejected under 35 U.S.C. § 101 as directed to patent-ineligible subject matter. Final Action 3. Claims 5, 6, 15—17, 48, and 55—58 stand rejected under 35 U.S.C. §112, second paragraph, as indefinite. Id. at 5. Claims 5, 6, 15—17, 48, and 55—58 stand rejected under 35 U.S.C. §103 over Hellinga.2 Id. at 6. DISCUSSION Except where otherwise indicated herein, we adopt the Examiner’s findings of fact, reasoning on scope and content of the claims and prior art, and conclusions set out in the Final Action and Answer. See Final Action 5— 10 and Answer 4—6. Only those arguments made by Appellants in the Appeal Brief and properly presented in the Reply Brief have been considered in this Decision. Arguments not so presented in the Briefs are waived. See 37 C.F.R. § 41.37(c)(l)(iv) (2015); see also Ex parte Borden, 2010 WL 191083 at *2 (BPAI 2010) (informative) (“Any bases for asserting error, whether factual or legal, that are not raised in the principal brief are waived.”). “[T]he examiner bears the initial burden, on review of the prior art or on any other ground, of presenting a prima facie case of unpatentability. 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). 2 US 2004/0229290 A1 (pub. Nov. 18, 2004) (“Hellinga”). 3 Appeal 2016-007854 Application 12/944,692 Patent-Eligibility “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); accord MPEP § 2106 (II) (discussing Diehr); see also 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 initial threshold is met, 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 97). Here, under Alice’s step one, the Examiner determined, “[t]he claims are directed to computational method of generating poses of a ligand molecule binding to a receptor molecule. As such, the claims are directed to an idea ‘of itself’, processing information and mathematical relationships which is an abstract idea.” Final Action 3. 4 Appeal 2016-007854 Application 12/944,692 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 of patent-ineligibility is without error because the claims are merely 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[ed] [were]... at their core, directed to the abstract idea of collecting, displaying, and manipulating data”). However, we conclude the facts compel a different outcome. We find the facts here are analogous to those of McRO, Inc. v. Bandai Namco Games America Inc., 837 F.3d 1299 (Fed. Cir. 2016). In McRO, the claims at issue were directed to “[a] method for automatically animating lip synchronization and facial expression of three-dimensional characters,” i.e., software for automating computer animation to better match a character’s mouth movements to what they say, including specially defined rules governing the animation morphing based on data on phonemes, which, when applied, produce lip synchronization. Id. 1307—08. As in McRO, “[h]ere, the claims are limited to rules with specific characteristics,” those rules here relate to optimization tools and accuracy 5 Appeal 2016-007854 Application 12/944,692 tools available to design and develop a molecule, e.g., a pharmaceutical, ideally paired to a target protein. Id.at 1313; see also Spec. ]Hf 14—15. The Specification describes, for example, the optimization tool as enabling the modification of specific ligand poses, receiving proteins, residues of the protein, simulated annealing, and simulated molecular dynamics, and describes the accuracy tool as enabling the modification of charges and other attractive/repulsive forces associated with the disclosed ligand-protein unit. Spec. 35—39. These tools, claimed as a part of the invention, are available to produce a set of simulated pairings (poses) of a ligand and protein of interest. We conclude the invention defined by the appealed claims is similar to that of McRO, as it was identified by the Federal Circuit,3 which our reviewing court concluded was not directed to an abstract idea. McRO 837 F.3d at 1316. Therefore, we conclude similarly here. “Because we find that claim [6] is not directed to ineligible subject matter, we do not reach Alice step two.” Id. (citing Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1339 (Fed. Cir. 2016). We reverse this rejection. Indefiniteness “[A] claim is indefinite when it contains words or phrases whose meaning is unclear,” i.e., “ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention.” In re 3 The Federal Circuit found, “allowing computers to produce ‘accurate and realistic lip synchronization and facial expressions in animated characters’ that previously could only be produced by human animators,” to be the claimed and specification-disclosed improvement of the invention. McRO, 837 F.3d at 1313 (quoting the patent’s specification at 2:49-50). 6 Appeal 2016-007854 Application 12/944,692 Packard, 751 F.3d 1307, 1310-13 (Fed. Cir. 2014); see also MPEP § 2173.02(1) (Rev. 07.2015, Nov. 2015) (advising examiners that a rejection for indefiniteness is appropriate “after applying the broadest reasonable interpretation to the claim, if the metes and bounds of the claimed invention are not clear”). We ask whether one of ordinary skill in the art would understand what is claimed when the claim is read in light of the Specification. Power-One, Inc. v. Artesyn Techs., Inc., 599 F.3d 1343, 1350 (Fed. Cir. 2010). “[I]f a claim is amenable to two or more plausible claim constructions, the USPTO is justified in requiring the applicant to more precisely define the metes and bounds of the claimed invention by holding the claim unpatentable under 35 U.S.C. § 112, second paragraph, as indefinite.” Ex parte Miyazaki, 89 USPQ2d 1207, 2008 WL 5105055, at *5 (BPAI 2008) (precedential). As explained in the MPEP § 2173.05(e), a “lack of clarity could arise [for example] where a claim refers to ‘said lever’ or ‘the lever,’ where the claim contains no earlier recitation or limitation of a lever and where it would be unclear as to what element the limitation was making reference.” This is an illustration of how the failure to provide adequate antecedent basis for claim elements can render a claim indefinite as unclear. The Examiner determined the claims are indefinite and identified several points of ambiguity or incoherence therein. Final Action 5. The Examiner determined that the claim 6 limitation relating to “selecting ... a tool” has no established relationship in the claim to other steps recited in the claim, i.e., “utilizing the determined tool,” and “computing energy calculations,” and “generating the second set of ligand poses.” Id. The 7 Appeal 2016-007854 Application 12/944,692 Examiner also determined that it is unclear how the claimed “utilizing the accuracy tool,” relating to modifying the ligand-protein system, can improve a process of calculating. Id. Appellants argue, after restating much of the language of claim 6, that “one skilled in the art would understand the energy calculation relates to the first set as realized with utilization of the determined tool.” App. Br. 15. Appellants also argue that the Specification explains how the accuracy tool works in improving the accuracy of calculations by modifying the charges (or other forces) considered in the process. Id. at 15—16. We agree with the Examiner; the claims are indefinite. The structure and language of claim 6 isolates the claimed “selecting, based on user preferences, a tool of a set of tools to utilize, wherein the set of tools includes an optimization tool and an accuracy tool” and the related, more descriptive limitations setting out the functionality of the claimed optimization tool and accuracy tool, from other steps of the method. Claim 6 requires that a set of tools is available and that it includes the claimed optimization tool and accuracy tool. However, the claim does not limit the tool set to the optimization and accuracy tools or require that one of these tools is actually selected and used in the claimed method; they are merely “include[d]” in the set. We find the claim indefinite because it is not clear how the “selected tool” relates to the claim term “the determined tool.” Put another way, “the determined tool” lacks antecedent basis. Given that the term “determine” is not a synonym for “select,” the skilled artisan would be compelled to ask: 8 Appeal 2016-007854 Application 12/944,692 what is “the determined tool,” how is it different from “the selected tool,” and what is its significance to the rest of the claimed method? Such nebulous claim language creates ambiguity and indefiniteness. We affirm the rejection. Obviousness “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSRInt’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). “[T]he analysis need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ.” Id. at 418. The Examiner determined that Hellinga taught and suggested the method of claim 6 and its dependent claims. Final Action 6. The Examiner specifically cited to Hellinga at claims 1, 2, 8, and 9, the abstract, and Tflf 9, 13, 22, 29, 38, 47, 62, 74, 82, 83-90, 95, 107-135, 143, 144, 179, 262, 276- 280 as teaching and suggesting the claimed “providing the first set of ligand poses,” “the set of tools including an optimization tool and an accuracy tool” as well as the claimed functionality of each tool, “utilizing [a] tool,” “computing energy calculations . . . ,” and “generating the second set of ligand poses . . . .” Id. at 6—10. Although all the claimed tools and their functionality were shown to be disclosed by Hellinga, Examiner determined that the step of “selecting, based on user preference, a tool of a set of tools,” was merely an obvious, optimizable feature based on a results effective variable for producing the most energy efficient simulated ligand-protein 9 Appeal 2016-007854 Application 12/944,692 permutation. Id. at 9. We conclude the Examiner has established a prima facie case that the claims would have been obvious over Hellinga.4 Appellants argue Hellinga and the method of claim 6 are fundamentally different. App. Br. 16. Appellants argue that the method disclosed by Hellinga is “a linear ‘A then B then C’ type of method,” while claim 6, as illustrated by Figure 1 of the Specification, is a branching- decision method that is not linear because of the “selecting, based on user preferences, a tool of a set of tools” step. Id. at 17—19. This argument is not persuasive. Claim 6 does not define a branching methodology, nor is its scope commensurate with Figure 1 of the Specification. As discussed above in relation to the indefmiteness rejection, claim 6 recites providing a set of tools and selecting a tool therefrom, but does not require that that tool be used and, even were the selected tool used, no other step of claim 6 relates to 4 Although we have determined supra that this claim limitation is indefinite, we nonetheless use our discretion in this case to address the prior art contentions. See, e.g., Supplementary Examination Guidelines for Determining Compliance With 35 U.S.C. § 112 and for Treatment of Related Issues in Patent Applications, 76 Fed. Reg. 7162, 7169 (Feb. 9, 2011) (advising examiners to interpret the claim and apply art with an explanation of how an indefinite term is interpreted under the principles of compact prosecution). In applying the cited art, we assume that the “determined tool” recited in claim 6 is or could be one of the identified “select[ed]” tools. As such, unlike in the case of In re Steele, 305 F.2d 859 (CCPA 1962), a determination of obviousness in this case does not require speculation as to the scope of the claims. Id. at 862-63 (holding that the Board erred in affirming a rejection of indefinite claims under 35 U.S.C. § 103(a), because the rejection was based on speculative assumptions as to the meaning of the claims). 10 Appeal 2016-007854 Application 12/944,692 such a usage. See Answer 5—6. Furthermore, Hellinga’s Figure 1, urged by Appellants as distinguishable from the invention of claim 6, is not definitional of the methods taught by the Hellinga, but merely “highlights major stages” thereof. Hellinga 112. Moreover, Appellants do not contest that Hellinga teaches all the basic elements of claim 6, but for the argued “selecting ... a tool” limitation; in view of this we note that Hellinga teaches producing all possible variations of ligand-protein postures/positions, including mutations, etc., and also teaches selecting subsets thereof for further evaluation, which renders selecting specific functionality and optimization or accuracy tools obvious. See Hellinga 19. Appellants also single out claim 5 as patentable over Hellinga. App. Br. 19. Appellants argue claim 5 requires iteratively repeating the method so as to provide a feedback loop as illustrated in the Specification’s Figure 1. Id. Appellants argue Hellinga does not teach looping back to previous steps in its method. Id. This argument is not persuasive. Hellinga, from the very first paragraph of its disclosure, teaches that its protein-ligand design method “can be iterated in multiple cycles.” Hellinga Abstr.; see also Final Action 8 (discussing this aspect of Hellinga). Moreover, Hellinga teaches that sub-portions of its method can be iterative, e.g., “iterative rounds of random mutagenesis,” which is similar to the optimization tool of the claims. Hellinga 1179; see also Final Action 8. For the reasons above, we affirm the obviousness rejection. SUMMARY The rejection of the claims as directed to patent-ineligible subject matter is reversed. 11 Appeal 2016-007854 Application 12/944,692 The rejection of the claims as indefinite is affirmed. The rejection of the claims as obvious is affirmed. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED 12 Copy with citationCopy as parenthetical citation