DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant's Amendment/Request for Reconsideration-After Non-Final Rejection filing of 2 February 2026, has been entered and fully considered.
Status of the Claims
Claim 29 is canceled.
Claims 1-28 are pending and are examined on the merits.
Priority
Priority is given to US 61/833,256 of the effective filing date of 10 June 2013.
Withdrawn Rejections/Objections
The objections to claims 1 and 23 in the Office action posted 11/6/2025 are withdrawn in view of claim amendments filed 2/6/2026.
The rejection of claims 1-28 under 35 U.S.C. 112(b) in the Office action posted 11/6/2025 are withdrawn in view of claim amendments filed 2/6/2026.
Claim Rejections - 35 USC § 101
This rejection is maintained from the previous Office action. Modifications are necessitated by claim amendments.
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.
Claims 1-28 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-28 are drawn to a process.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
Assembling experimentally derived data comprising a multiplicity of measurements of amino acid physicochemical properties;
This step recites manipulation of data, which can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Producing a correlation matrix of the experimentally derived data;
This step recites manipulation of data of creating a matrix, and a mathematical calculation of correlations. Therefore, this step equates to an abstract idea of mental processes and mathematical concepts.
Deriving by Principal Component Analysis multiple uncorrelated dimensionless, weighted and ranked proxy descriptors to describe at least 80% of the variance in said physicochemical properties of individual amino acids;
This step recites manipulation of data of deriving descriptors, and mathematical calculations of Principal Component Analysis. Therefore, this step equates to an abstract idea of mental processes and mathematical concepts.
Using said proxy descriptors to describe individual amino acids in a set of peptides each of which comprises a specific cleavage site dimer experimentally determined to be cleaved, and to describe the individual amino acids in a set of peptides each of which comprises the same cleavage site dimer experimentally determined to be uncleaved;
This step recites the preparation of input data through encoding (the descriptors are interpreted as “mathematical expressions” according disclosure at page 4 lines 2-5), which comprise the attributes describing individual amino acids. Hence this step recites re-organizing data and manipulation of data by deriving descriptors. This step can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Comparing, via probabilistic modeling, the amino acid descriptors of said peptides comprising said experimentally determined cleaved and uncleaved cleavage site dimers to derive a cleavage prediction equation for said specific cleavage site dimer based on that peptide set;
This step recites mathematical calculations of probabilistic modeling, using the encoded amino acid attributes as input. Therefore, this step equates to an abstract idea of mathematical concepts.
Repeating the steps of (iv) and (v) multiple times, each time with a different set of peptides that comprise the same cleavage site dimer and are experimentally determined to be cleaved or not cleaved, thereby deriving an ensemble of independently derived peptidase cleavage prediction equations for said specific cleavage site dimer;
This step repeats the previous two steps. Therefore, this step equates to an abstract idea of mental processes and mathematical concepts.
Repeating the process of (iv) to (vi) to derive ensembles of independently derived prediction equations for every possible cleavage site dimer up to a total of 400 such ensembles;
This step repeats the previous three steps. A lot of math with a lot of data performed on a computer does not take the claims outside the realm of abstract ideas. The purpose of computers is to facilitate processing efficiency. Therefore, this step equates to an abstract idea of mental processes and mathematical concepts.
Applying said proxy descriptors from said Principal Component Analysis to describe individual amino acids in said target polypeptide sequence.
This step recites manipulation of the PCA (Principal Component Analysis) data by encoding through the descriptors. Therefore, this step equates to an abstract idea of mental processes.
Deriving vectors to describe a plurality of peptides of defined length in said target polypeptide.
This step recites manipulation of data by deriving vectors, which can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Via said computer processor applying said up to 400 ensembles of independently derived peptidase cleavage prediction equations to said plurality of peptides of defined length from said target polypeptide to predict a plurality of peptidase cleavage sites in said target polypeptide;
This step recites “to predict a plurality of peptidase cleavage sites”, which under a Broadest Reasonable Interpretation (BRI), can be a linear regression to calculate probabilities. Therefore, this step equates to an abstract idea of mathematical concepts.
Identifying, by consensus of the ensembles of prediction equations, the probability of cleavage at any given cleavage site dimer in said target polypeptide;
This step recites decision-making activities (identifying) and mathematical calculations (equations, probability). Therefore, this step equates to an abstract idea of mental processes and mathematical concepts.
Defining amino acid subsets in the target polypeptide that are predicted to be cleaved by a peptidase;
This step recites a decision-making activity (defining a subset), which can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Substituting one or more amino acids in the defined amino acid subsets in the target polypeptide to change the probability of peptidase cleavage.
This step recites an activity that can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Step 2A Prong Two: Consideration of Practical Application
The claimed method steps do not include any additional elements that integrate the recited judicial exceptions (abstract ideas here) into a practical application. The synthesizing and administering the variant target polypeptide are tangentially recited to the recited abstract idea steps. Obtaining amino acid sequence of a target peptide is a necessary step for data modeling and prediction. The claim recites administering the variant target polypeptide to the subject, which is neither specific regarding the disease, nor particular regarding the treatment.
Additionally, there is no relationship between “substituting one or more amino acids in the defined amino acid subsets in the target polypeptide to change the probability of peptidase cleavage” and “synthesizing a variant of the target polypeptide comprising the substituted amino acids”. The single variant of the target peptide being synthesized is not necessarily the peptide created in the previous “substituting” step.
Consequently, there is a gap and therefore no integration of the abstract idea step into the step of synthesizing which would be the practical application.
In these two regards, the judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The preamble of claim 1 recites a method of administering a synthetic peptide to a subject, which a conventional activity in the clinical industry.
The following additional elements are recited in claims:
obtaining an amino acid sequence for a target polypeptide;
synthesizing the variant polypeptide comprising the substituted amino acids; and
administering the variant polypeptide to the subject to vaccinate or treat the subject for a disease or condition.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because 1) data inputting is an insignificant extra-solution activity (MPEP 2106.05(g)) and 2) synthesizing and administering a synthetic peptide to a subject are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself.
Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Applicant’s Arguments
In the Remarks filed 2/6/2026, Applicant argues (1st page, lower part through 2nd page, 1st para) that amended claim 1 now recites:
synthesizing the variant polypeptide comprising the substituted amino acids; and
administering the variant polypeptide to the subject to vaccinate or treat the subject for a disease or condition.
Hence claims are 101 eligible because claim 1 recites variant polypeptides used for vaccination or treatment.
In response, Applicant’ argument is not persuasive. With respect to a specific treatment, synthesizing and administering the variant target polypeptide are tangentially recited to the recited abstract idea steps. The claim recites administering the variant target polypeptide to the subject, which is neither specific regarding the disease, nor particular regarding the treatment.
When considering transformation, there is no relationship between “substituting one or more amino acids in the defined amino acid subsets in the target polypeptide to change the probability of peptidase cleavage” and “synthesizing a variant of the target polypeptide comprising the substituted amino acids”. There is no connection between a single variant of the target peptide being synthesized and the previous step where “one or more” amino acids are substituted. The previous step is about changed probabilities of cleavage at many amino acid sites and the subsequent step is about “synthesizing a variant of the target polypeptide”. The later step does not necessarily have any relation to the previous step. There is still a gap between these two steps. Consequently, there is no integration into a practical application.
In these two regards, the judicial exception is not integrated into a practical application because the judicial exceptions are not captured and reflected 100% in the additional elements.
Therefore, the 101 rejection is maintained.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights