DETAILED ACTION
Comments
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claims 1-12 are pending and examined in the instant Office action.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The term “proximity” in each independent claim is a relative term which renders the claim indefinite. The term “proximity” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Absent a limiting description from the specification on the criteria for amino acid positions being in proximity, it is interpreted that any two amino acid positions are in proximity.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim(s) 1-12 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-4 are drawn to methods, claims 5-8 are drawn to one or more non-transitory computer-readable storage media, and claims 9-12 are drawn to systems comprising computers.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
The independent claims recite the mental steps of arranging, determining positions of, and indexing a plurality of amino acids based, in part, on angles and states.
The independent claims recite the mental step of using dynamic programming to determine the three dimensional structure of the plurality of amino acids.
Claims 2, 6, and 10 recite the mathematical limitations of using a multivariate Gaussian distribution comprising a mean vector and a covariance matrix.
Claims 3, 7, and 11 recite the mental step of learning positional data.
Claims 4, 8, and 12 recite the mental step of using one-hot representations to assist with the learning.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-12 recite(s) an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-12 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-12 is/are not patent eligible.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
35 U.S.C. 103 Rejection #1:
Claim(s) 1, 5, and 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kentaro [GB 2411655 A; on 892 form] in view of Brooks et al. [Journal of Computational Chemistry, volume 4, 1983, pages 187-217; on 892 form].
Claim 1 is drawn to a computer-implemented method for facilitating predicting a three-dimensional structure of an amino acid sequence. The method comprises determining pairs of angles, indexing, and determining the states of a plurality of amino acids in proximity. The method comprises using dynamic programming to determining the three dimensional structure of the amino acids.
Claim 5 is drawn to similar subject matter as claim 1, except claim 5 is drawn to one or more non-transitory computer-readable storage media.
Claim 9 is drawn to similar subject matter as claim 1, except claim 9 is drawn to a system comprising computers.
The document of Kentaro studies a system for predicting the three-dimensional structure of proteins [title]. Figure 1 of Kentaro illustrates the computer limitations of the claims. The abstract of Kentaro teaches positioning of proximate amino acids based on mathematical correlation algorithms involving matrices and vectors.
Kentaro does not teach dynamic programming involving angles of amino acids.
The document of Brooks et al. studies the force field CHARMM as a program for macromolecular energy, minimization, and dynamics calculations [title]. Figure 2 and the equations of Brooks et al. teach the roles of bonds angles of amino acids in dynamic programming determining three-dimensional structure of the amino acid sequence.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the protein three-dimensional structure calculation of Kentaro by use of the dynamics calculations involving bond angles of Brooks et al. wherein the motivation would have been that the tools of Brooks et al. facilitate the three-dimensional structure calculation of Kentaro [Figure 2 and equations of Brooks et al.]. There would have been a reasonable expectation of success in combining Kentaro and Brooks et al. because both studies are analogously applicable to determining three-dimensional protein structures using calculations.
35 U.S.C. 103 Rejection #2:
Claim(s) 2, 6, and 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kentaro in view of Brooks et al. as applied to claims 1, 5, and 9 above, in further view of Hunter [US PGPUB 2005/0192754 A1; on 892 form].
Claims 2, 6, and 10 are further limiting wherein determining pairs of angles based on a multivariate Gaussian distribution comprising a mean vector and a covariance matrix.
Kentaro and Brooks et al. make obvious calculating the three dimensional structure of the protein using calculations, as discussed above. The abstract of Kentaro teaches positioning of proximate amino acids based on mathematical correlation algorithms involving covariance matrices and vectors.
Kentaro and Brooks et al. do not teach associating Gaussians with the vectors.
The document of Hunter studies protein sequence signals and their applications [title]. The abstract of Hunter teaches associating signals with protein structure. Paragraph 134 of Hunter teaches associating Gaussians with signals.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the protein three-dimensional structure calculation of Kentaro and the dynamics calculations involving bond angles of Brooks et al. by use of the Gaussians of Hunter wherein the motivation would have been that the analysis of Hunter facilitates the three-dimensional structure calculation of Kentaro and Brooks et al. [abstract and paragraph 134 of Hunter]. There would have been a reasonable expectation of success in combining Kentaro, Brooks et al., and Hunter because all three studies are analogously applicable to determining three-dimensional protein structures.
35 U.S.C. 103 Rejection #3:
Claim(s) 3, 7, and 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kentaro in view of Brooks et al. in view of Hunter as applied to claims 1-2, 5-6, and 9-10 above, in further view of Costa et al. [Intelligent Data Analysis, volume 2, 1998, pages 265-286; on 892 form].
Claims 3, 7, and 11 are further limiting wherein the three-dimensional structure is based on properties learned from amino acid training data.
Kentaro, Brooks et al. and Hunter make obvious calculating the three dimensional structure of the protein using calculations, as discussed above.
Kentaro, Brooks et al., and Hunter do not teach involving machine learning the calculations.
The document of Costa et al. teaches a prediction method for nominal variable. The abstract and section 4.1 of Costa et al. teaches applying mathematical algorithms based on machine learning to predict the secondary structures of amino acids.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the protein three-dimensional structure calculation of Kentaro, the dynamics calculations involving bond angles of Brooks et al., and the Gaussians of Hunter by use of the machine learning of Costa et al. wherein the motivation would have been that the analysis of Costa et al. facilitates the three-dimensional structure calculation of Kentaro, Brooks et al., and Hunter [abstract and Section 4.1 of Costa et al.]. There would have been a reasonable expectation of success in combining Kentaro, Brooks et al., Hunter, and Costa et al. because all four studies are analogously applicable to determining three-dimensional protein structures.
35 U.S.C. 103 Rejection #4:
Claim(s) 4, 8, and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kentaro in view of Brooks et al. in view of Hunter in view of Costa et al. as applied to claims 1-3, 5-7, and 9-11 above, in further view of Prieditis [US PGPUB 2020/0184371; on 892 form].
Claims 4, 8, and 12 are further limiting wherein the machine learning is based on one-hot representations.
Kentaro, Brooks et al., Hunter, and Costa et al. make obvious calculating the three dimensional structure of the protein using machine learning, as discussed above.
Kentaro, Brooks et al., Hunter, and Costa et al. do not teach that the machine learning uses one-hot representations.
The document of Prieditis studies a method and system for facilitating combining categorical and numerical variables in machine learning [title]. Paragraphs 5-6 of Prieditis teach use of one-hot representations.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the protein three-dimensional structure calculation of Kentaro, the dynamics calculations involving bond angles of Brooks et al., the Gaussians of Hunter, and the machine learning of Costa et al. by use of the one-hot representations of Prieditis wherein the motivation would have been that the one-hot representations facilitate machine learning [abstract and paragraphs 5-6 of Prieditis]. There would have been a reasonable expectation of success in combining Prieditis with Kentaro, Brooks et al., Hunter, and Costa et al. because the one-hot representations in machine learning of Prieditis are robust, and are generally applicable to applying machine learning to determining protein structure of Kentaro, Brooks et al., Hunter, and Costa et al.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/Primary Examiner, Art Unit 1686 18 November 2025