Ex Parte Zhou et al

Patent Trials and Appeals BoardApr 10, 2019

13188598 - (D) (P.T.A.B. Apr. 10, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 13/188,598 07/22/2011 23623 7590 04/12/2019 AMIN, TUROCY & WATSON, LLP 200 Park A venue Suite 300 Beachwood, OH 44122 FIRST NAMED INVENTOR Weiqiang Zhou 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. PWG/PA2431201 l/CITYP123US 8509 EXAMINER SKIBINSKY, ANNA ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 04/12/2019 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): hmckee@thepatentattomeys.com rveri@thepatentattomeys.com docket@thepatentattomeys.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte WEIQIANG ZHOU and HONG Y AN 1 Appeal 2018-004159 Application 13/188,598 Technology Center 1600 Before RYAN H. FLAX, RACHEL H. TOWNSEND, and CYNTHIA M. HARDMAN, Administrative Patent Judges. HARDMAN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. Â§ 134(a) involving claims to modeling and analyzing a binding interface between two molecules, which have been rejected as being directed to patent-ineligible subject matter. We have jurisdiction under 35 U.S.C. Â§ 6(b ). We REVERSE. 2 1 Appellants identify City University of Hong Kong as the real party in interest. (Appeal Br. 2.) 2 Our Decision refers to the Final Office Action, mailed Apr. 19, 2017 ("Final Act."); Appeal Brief, filed Sept. 18, 2017 ("Appeal Br."); Examiner's Answer, mailed Jan. 11, 2018 ("Ans."); Reply Brief, filed Mar. 12, 2018 ("Reply Br."); and Specification, filed July 22, 2011 ("Spec."). Appeal 2018-004159 Application 13/188,598 STATEMENT OF THE CASE According to the Specification, "[i]nteractions between different biomolecules, such as proteins, deoxyribonucleic acid (DNA), and ligands, are essential for many biological processes." (Spec. ,r 2.) The Specification further states: "Traditionally, biological experiments have been used to determine whether a drug molecule is a ligand that will interact with or dock to a given protein. However, these biological experiments are both costly and time consuming." (Id. at ,r 3.) The invention "provides a fully automated algorithm to construct the interface surface between two biomolecules involved in an interaction (e.g., protein-protein interactions, protein-DNA interactions, protein-ligand interactions, and DNA-ligand interactions)." (Id. at ,r 45.) Claims 1, 3-5, 8-10, 12-16, 20-22 and 29-35 are on appeal. Claim 1 is illustrative and reads as follows: 1. A method, comprising: generating, by a system comprising a processor, a first three-dimensional model of a complex, wherein the complex comprises a first molecule and a second molecule, and wherein the first-three dimensional model comprises a first alpha shape; identifying, by the system, a first set of atoms located on a surface of the first alpha shape, wherein the surface of the first alpha shape corresponds to at least a first portion of a first surface of the first molecule and at least a second portion of a second surface of the second molecule; generating, by the system, a second three-dimensional model of the first molecule, wherein the second three- dimensional model comprises a second alpha shape; identifying, by the system, a second set of atoms located on a surface of the second alpha shape, wherein the surface of 2 Appeal 2018-004159 Application 13/188,598 the second alpha shape includes at least the first portion of the first surface of the first molecule; determining, by the system, a third set of atoms included in the second set of atoms and not included in the first set of atoms; and generating, by the system, a third three-dimensional model of a binding interface between the first molecule and the second molecule in the complex based on the second alpha shape and the third set of atoms, wherein the third three- dimensional model e [sic] comprises the third set of atoms. (Appeal Br. 64, Claims Appendix.) Claims 1, 3-5, 8-10, 12-16, 20-22 and 29-35 stand rejected under 35 U.S.C. Â§ 101. (Final Act. 2.) DISCUSSION The Examiner found that "[a]s a whole, the claims are drawn to a computational method of mathematical algorithm based molecular modeling." (Final Act. 3; see also Ans. 4.) Specifically, the Examiner stated: The recited three dimensional model is based on mathematical relationships, data, and parameters. It can be represented with equivalent accuracy using mathematical constructs such as formulas and numerical descriptors/parameters representing relationships between the molecules in the complex. That is why it is deemed to be an abstract idea. (Final Act. 4.) The Examiner also found that the claims recite mental processes, stating: The recited steps, including determining of the three dimensional model are drawn to geometrical and mathematical calculations, though complex in nature, can be performed outside of a computer and do not necessitate a computer. ... It is the Examiner's position that each of the claimed process 3 Appeal 2018-004159 Application 13/188,598 steps (absent the generic computer) could be carried out as a mental process or with the aid of paper/pen. (Id. at 8, emphasis in original.) The Examiner further found that "[ t ]he claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception," because, inter alia, certain of the claims recite "mere instructions used to implement the idea on a computer and recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry." (Id. at 3--4.) In response, Appellants argued, among other things, that [C]laim 1 is directed to generating a three-dimensional model of a binding interface between two molecules that comprise the specific atoms (i.e., the third set of atoms) that are included on the binding interface. In this regard, claim 1 is not directed to 'a computational method of mathematical algorithm based molecular modeling' as alleged by the Examiner. ( Appeal Br. 17, emphases in original.) Appellants also argued, among other things, that the claimed subject matter "serves to improve the existing technology by providing for automatically identifying molecular interfaces, and automatically generating a model that corresponds to the binding interface and specifically includes the atoms of the binding interface." (Appeal Br. 23, emphasis in original.) Appellants cited various paragraphs of the Specification and two inventor affidavits3 to support their argument that the claimed techniques "achieve greater accuracy and efficiency than prior art methods with respect 3 Declaration under 37 C.F.R. Â§ 1.132, filed June 29, 2015 ("Affidavit I"); Declaration under 37 C.F.R. Â§ 1.132, filed Jan. 6, 2016 ("Affidavit II"). 4 Appeal 2018-004159 Application 13/188,598 to at least the identification of the atoms which constitute the binding interface and the resulting molecular model of the binding interface" between two molecules. (Id. at 24.) We agree with Appellants that the Examiner has not established that the claimed subject matter is patent-ineligible. An invention is patent- eligible if it claims a "new and useful process, machine, manufacture, or composition of matter." 35 U.S.C. Â§ 101. However, the Supreme Court has long interpreted 35 U.S.C. Â§ 101 to include implicit exceptions: "[l]aws of nature, natural phenomena, and abstract ideas" are not patentable. See, e.g., Alice Corp. v. CLS Bankint'l, 573 U.S. 208,216 (2014). In determining whether a claim falls within an excluded category, we are guided by the Supreme Court's two-step framework, described in Mayo and Alice. Id. at 217-18 ( citing Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 75-77 (2012)). In accordance with that framework, we first determine what concept the claim is "directed to." See Alice, 573 U.S. at 219 ("On their face, the claims before us are drawn to the concept of intermediated settlement, i.e., the use of a third party to mitigate settlement risk."); see also Bilski v. Kappas, 561 U.S. 593, 611 (2010) ("Claims 1 and 4 in petitioners' application explain the basic concept of hedging, or protecting against risk."). Concepts determined by the courts to be abstract ideas, and thus patent ineligible, include certain methods of organizing human activity, such as fundamental economic practices (Alice, 573 U.S. at 219-20; Bilski, 561 U.S. at 611); mathematical formulas (Parker v. Flook, 437 U.S. 584, 594--95 (1978)); and mental processes ( Gottschalk v. Benson, 409 U.S. 63, 69 (1972)). Concepts determined to be patent eligible include physical and 5 Appeal 2018-004159 Application 13/188,598 chemical processes, such as "molding rubber products" (Diamond v. Diehr, 450 U.S. 175, 192 (1981)); "tanning, dyeing, making waterproof cloth, vulcanizing India rubber, smelting ores" (id. at 184 n. 7 ( quoting Corning v. Burden, 56 U.S. 252, 267---68 (1854))); and manufacturing flour (Benson, 409 U.S. at 69 (citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))). In Diehr, the claim at issue recited a mathematical formula, but the Supreme Court held that "[a] claim drawn to subject matter otherwise statutory does not become nonstatutory simply because it uses a mathematical formula." Diehr, 450 U.S. at 176, 191 ("We view respondents' claims as nothing more than a process for molding rubber products and not as an attempt to patent a mathematical formula."). Having said that, the Supreme Court also indicated that a claim "seeking patent protection for that formula in the abstract ... is not accorded the protection of our patent laws,[] and this principle cannot be circumvented by attempting to limit the use of the formula to a particular technological environment." Id. ( citing Benson and Flook); see also id. at 187 ("It is now commonplace that an application of a law of nature or mathematical formula to a known structure or process may well be deserving of patent protection."). If the claim is "directed to" an abstract idea, we tum to the second step of the Alice and Mayo framework, where "we must examine the elements of the claim to determine whether it contains an 'inventive concept' sufficient to 'transform' the claimed abstract idea into a patent- eligible application." Alice, 573 U.S. at 221 (quotation marks omitted). "A claim that recites an abstract idea must include 'additional features' to ensure 'that the [claim] is more than a drafting effort designed to 6 Appeal 2018-004159 Application 13/188,598 monopolize the [abstract idea]."' Id. (quoting Mayo, 566 U.S. at 77). "[M]erely requir[ing] generic computer implementation[] fail[ s] to transform that abstract idea into a patent-eligible invention." Id. The United States Patent and Trademark Office recently published revised guidance on the application of section 101. US PTO' s 2019 Revised Patent Subject Matter Eligibility Guidance ("Guidance"). 4 Under the Guidance, in determining what concept a claim is "directed to," we first look to whether the claim recites: (1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes); and (2) additional elements that integrate the judicial exception into a practical application (see MPEP Â§ 2106.05(a}- (c), (e}-(h)). Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an "'inventive concept' sufficient to 'transform"' the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim: (3) adds a specific limitation beyond the judicial exception that are not "well-understood, routine and conventional in the field" (see MPEP Â§ 2106.05(d)); or (4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. 4 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019). 7 Appeal 2018-004159 Application 13/188,598 See Guidance, 84 Fed. Reg. at 54--56. Guidance Step 2A, Prong 1 Pursuant to the Guidance, we begin by determining whether the claims recite any judicial exception(s) to patent eligibility. Guidance, 84 Fed. Reg. at 54. The Examiner found that the claims recite abstract ideas. (See, e.g., Final Act. 4.) We disagree. We conclude that the claims do not recite any of the three judicially- excepted groupings of abstract ideas. Guidance, 84 Fed. Reg. at 52. First, the claims do not recite any method of organizing human activity such as fundamental economic practices. Second, although the Examiner contended that the claims recite mental processes (see, e.g., Final Act. 8; Ans. 6), the Examiner has not made any factual findings substantiating the contention that the claims could practicably be performed in the human mind or with pen and paper, and therefore amount to a mental process. See Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1147, 1148 (Fed. Cir. 2016) ( noting that, with respect to the claimed method of changing one description of a level sensitive latch into another, "the patent specification itself' demonstrated that "the method can be performed mentally or with pencil and paper" and that the inventors "admitted to performing the steps mentally themselves"); see also CyberSource Corp. v. Retail Decisions, Inc., 654 F .3d 1366, 1376 (Fed. Cir. 2011) (noting that in SiRF Tech., Inc. v. Int'! Trade Com'n, 601 F.3d 1319, 1331 (Fed. Cir. 2010) the claims found patent eligible, despite reciting a method for calculating, were "not dealing with ... a method that [ could] be performed without a machine" and that there was "no evidence ... that the calculations [ could] be performed entirely in the human mind," and similarly noting that in Research Corp. Techs. v. 8 Appeal 2018-004159 Application 13/188,598 Microsoft Corp., 627 F.3d 859 (Fed. Cir. 2010), "the method [for the halftoning of gray scale images by utilizing a pixel-by-pixel comparison of the image against a blue noise mask] required the manipulation of computer data structures ( e.g., the pixels of a digital image and a two-dimensional array known as a mask) and the output of a modified computer data structure (a halftoned digital image), the method could not, as a practical matter, be performed entirely in a human's mind"). The final category of abstract ideas that has been identified by the courts is mathematical concepts. See Guidance, 84 Fed. Reg. at 52. We find that the claims do not recite any mathematical concept, such as a specific mathematical algorithm or formula (see Flook, 437 U.S. at 586; Diehr, 450 U.S. at 187). To be sure, certain claim limitations, such as generating a "three-dimensional model" comprising an "alpha shape" in claim 1; generating a "three-dimensional alpha shape" in claim 14; and "generating a first Delaunay triangulation" in claim 3 1, are based on mathematical relationships, formulas, or calculations, but the mathematical relationships, formulas, or calculations are not explicitly recited in the claims. Accordingly, in light of the Guidance, we find that the claims do not recite an abstract idea that would make them patent-ineligible under 35 U.S.C. Â§ 101. Guidance, 84 Fed. Reg. at 54 ("If the claim does not recite a judicial exception, it is not directed to a judicial exception (Step 2A: NO) and is eligible.") (Emphasis added.) Guidance Step 2A, Prong 2 Even if the claims were interpreted as reciting mathematical concepts, and therefore an abstract idea, under prong 2 of Step 2A of the Guidance, we find that the claims integrate any recited mathematical concept into a 9 Appeal 2018-004159 Application 13/188,598 practical application. Specifically, the steps in independent claims 1, 14, and 16 result in "identification of the atoms which constitute the binding interface [between two molecules,] and the generation of [a] molecular model of the binding interface." (Appeal Br. 23.) According to the Specification, this makes it possible to "determine whether a ligand will dock to a given protein in an efficient and cost-effective manner." (Spec. Appellants assert that the "automated results" of the claims "are substantial technical improvements [] over existing manual techniques used in molecular modeling." (Appeal Br. 23, emphasis in original.) Indeed, the Specification discloses that the claimed subject matter improves on "[t]raditional methods of determining whether a ligand will dock to a given protein, such as biological experiments, which are time consuming and costly." (Spec. ,r 71.) Appellants also assert that "the claimed techniques achieve greater accuracy and efficiency than prior art methods with respect to at least the identification of the atoms which constitute the binding interface and the resulting molecular model of the binding interface." (Appeal Br. 24.) The Specification supports this argument by disclosing that, compared to prior art methods that use distances among atoms to predict interactions between two molecules, the claimed subject matter "is 3- D in nature and can be utilized to compute many statistical, topological, and geometric features that can provide high prediction power." (Id. ,r 45.) These asserted improvements in molecular modeling that determine the binding interface between two molecules are also supported by testimony from the inventors. The inventors explained the improvements of 10 Appeal 2018-004159 Application 13/188,598 the claimed subject matter over prior art methods, and compared the prediction accuracy with prior art methods: Traditional molecular modeling methods used spheres to represent atoms and used distance between atoms to characterize the binding interface of two molecules .... However, the interface obtained relied much on the selection of the threshold .... On the contrary, our method is nonparametric and captures a more precise interface between two molecules. (Affidavit I 4; see also Affidavit II at, e.g., 4---6 ( comparing claimed method to prior art methods and concluding that claimed method "brings highly significant better results than the conventional distance based method").) Accordingly, in light of the Specification and the inventors' testimony, we find that the claimed subject matter reflects an improvement in a specific molecular modeling technology, i.e., three-dimensional model of a binding interface between the first molecule and the second molecule. See Guidance, 84 Fed. Reg. at 55. As such, even if claim limitations such as those directed to generation of three-dimensional models, alpha shapes, or Delaunay triangulations were interpreted to recite abstract ideas, we find that the claims use this subject matter in a specific manner and impose a meaningful limit on any judicial exceptions by limiting their use to a practical application, which is the generation of a three-dimensional model or alpha shape of the binding interface between two molecules. The practical application recited by the claims when viewed as a whole is more than a drafting effort to monopolize the use of mathematical concepts. Thus, we find that the claims as a whole are not "directed to ... [a] patent-ineligible concept." Alice, 573 U.S. at 217. 11 Appeal 2018-004159 Application 13/188,598 SUMMARY We reverse the rejection of claims 1, 3-5, 8-10, 12-16, 20-22 and 29-35 under 35 U.S.C. Â§ 101. REVERSED 12