Notice of Pre-AIA or AIA Status
Applicant’s arguments, filed 4/30/2026, have been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Applicants have amended their claims, filed 4/30/2026, and therefore rejections newly made in the instant office action have been necessitated by amendment.
Applicant has newly added claims 10-11, which have been acknowledged and entered.
Claims 1-11 are the current claims hereby under examination.
Claim Rejections - 35 USC § 112-modified necessitated by amendment
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 1-11 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.
A claim fails to satisfy the statutory requirement and is thus invalid for indefiniteness if its language, when read in light of the specification and the prosecution history, “fail[s] to inform, with reasonable certainty, those skilled in the art about the scope of the invention.” Nautilus, Inc. v. Biosig Instruments, Inc., 134 S. Ct. 2120, 2124 (2014). In Nautilus, the Supreme Court expressly rejected that “insolubly ambiguous” or “amenable to construction” standard. Nautilus, 134 S. Ct. at 2124. Rather, the Court “h[e]ld that a patent is invalid for indefiniteness if its claims, read in light of the specification delineating the patent, and the prosecution history, fail to inform, with reasonable certainty, those skilled in the art about the scope of the invention.” Id. The Court explained further: “[i]t cannot be sufficient that a court can ascribe some meaning to a patent’s claim; the definiteness inquiry trains on the understanding of a skilled artisan at the time of the patent application, not that of a court viewing matters post hoc.” Id. at 2130. “A patent must be precise enough to afford clear notice of what is claimed, thereby ‘appris[ing] the public of what is still open to them. Notably a claim is indefinite if its language “might mean several different things and no informed and confident choice is available among the contending definitions.” Id. At 2130 n.8. Although the Court recognized that “[s]ome modicum of uncertainty” may be tolerated, id. at 2128, the patent and prosecution history must disclose a single known approach or establish that, where multiple known approaches exist, a person having ordinary skill in the art would know which approach to select. See Teva, 789 F.3d at 1341, 1344–45 (holding claim indefinite where molecular weight could be measured three different ways and would yield different results and the patent and prosecution history did not provide guidance as to which measure to use).
Claims 1 and 5 (and all claims dependent therefrom) recite the steps of “estimating binding free energy of the target interface by feeding, into a model for estimating binding free energy……” wherein the step has been deemed as vague and indefinite. The instant claims are process claims and not result claims. Therefore, the steps are required to define how the process steps end in the recited results. For example, the claims are required to define how the model processes the different data values to arrive at the result. In other words what algorithm is used for ingesting the atomic distance related to the target interface, atomic interaction force of the target interface and the relevant information to estimate binding free energy. The steps are clear with regards to the results they produce, but are not clear as to exactly how they are produced. There is no algorithm or prose equivalent recited for performing said estimation. Without defining the steps of the model it is not possible to have a clear measure of what applicant’s regard as the invention so that it can be determined whether the claimed invention meets all the criteria for patentability. The lacking of properly defined method steps further makes the scope of the claim unclear so that a person of ordinary skill in the art would be informed of the boundaries of what constitutes infringement of the patent.
Furthermore, the specification at pages 23-24 (and fig. 4) only generally describes using training data to train a model and validating it. The specification describes the general data for what is input to training a model, but provides no details as to how that data is trained. The specification further refers to fig. 4 for model validation, which only shows a graph of a result of validation but does not describe how the model is specifically trained. However, there are innumerable many ways of implementing of training models wherein the multiple methods of implementation may lead to different results. Without guidance as to which method should be used renders the steps/system/claims indefinite. In addition, the specification does not provide any guidance on which method should be used or even whether the possible universe of methods is limiting. Because the variety of methods of implementing training a model and using a model do not produce the same results, the method chosen for implementation could affect whether or not a given product infringes the claims (see CAFC Dow v Nova August 2015). Clarification via clearer claim wording is required.
Response to Arguments
Applicant's arguments filed 4/30/2026 have been fully considered but they are not persuasive. Applicant argues that the amendment to cancel the limitation of “wherein the model for estimating binding free energy is implemented by a deep neural network (DNN) causes said claim 1 to be definite.
Applicant argument is not found persuasive as the limitation has only served to broaden the scope of the model from one that uses a DNN now to an even broader scope of using any and all models.
Applicant further argues that the specification describes model training and the claimed method is a sequence of calculation steps and therefor a skilled person would understand each of the calculation steps.
Applicant argument is not found persuasive as each of the steps may be understood, but what is not clear is how the result of each of those calculation steps are used in “a model for estimating binding free energy” using the data that is input into it as described above in the instant rejection of claims under 112 (b) above.
Claim Rejections - 35 USC § 101-maintined
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 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
the claimed invention is directed to determining whether a fetus has a chromosomal aneuploidy or a generating a classification model for doing so without significantly more.
Analysis of independent claims 1:
Step 1 of the subject matter eligibility test (see MPEP 2106.03).
Claims 1-4 are directed to a method and claims 5-9 are directed to a system comprising a storage device and connected processor to implement the model on the storage device, which describes one or more of the four statutory categories of patentable subject matter, i.e., a process/machine. Therefore, further consideration is necessary.
Step 2A of the subject matter eligibility test (see MPEP 2106.04).
Prong One: Claim 1 recites an abstract idea. In particular, the claim recites the following:
obtaining spatial coordinate sets data;
b. calculating Euclidean distances;
c. identifying interaction interfaces between residues;
d. selecting an interaction interface;
e. determining a mutant residue;
f. obtaining inferred rotation angles;
g. calculating spatial coordinate sets;
h. calculating a value of atomic-level energy and Euclidean distance based on the spatial coordinate sets for the target interfaces and every two heavy atoms respectively of the mutant residue and paired residue of the mutant protein complex;
i. calculating an atomic distance related to the target interface and an atomic interaction force of the target interface;
j. obtain relevant information that is related to the specific residue of the reference protein complex and mutant residue of the mutant protein complex from amino acid physicochemical properties data; and
k. estimating binding free energy of the target interface using a model.
These elements recited in claims 1 and 5 are drawn to an abstract idea since they involve a mental process that can be practically performed in the human mind using pen and paper and/or they involve mathematical concepts in the form of mathematical relationships, mathematical formulas or equations, and/or mathematical calculations. The claims do not require overly large mutant protein complexes, so seemingly said method can be applied to short mutant protein complexes involving small numbers of amino acids making said claims capable of being performed using pen and paper.
The identified abstract steps, recited at the high level of generality, do not suggest an undue level of complexity for a person with ordinary skill in the art to be practically performed in the human mind with the aid of pen and paper.
Prong Two: Claim 1 does not recite additional elements that integrate the exception into a practical application. Therefore, the claims are “directed to” the abstract idea.
There are no identified limitations beyond the abstract idea above in claims 1-4 or beyond the use of a computer to implement the abstract idea (claims 5-9). Claims 5-9 have the same analysis as above, but with the addition of the method being carried out on a computer. Patenting abstract ideas cannot be circumvented by attempting to limit the use [the idea] to a particular technological environment. In the instant claims, the computer and/or program/product amount to mere instruction to implement an abstract idea. The hardware recited by the system claims do not offer a meaningful limitation beyond generally linking “the use of the method to a particular technological environment,’ that is, implementation via computers.” see Alice Corp v. CLS Bank Int’l 573 U.S. (2014).
Therefore there is no identifiable practical application because the abstract idea is not applied, relied on, or used in a meaningful way. The processing performed remains in the abstract realm, i.e., the result is not used for a treatment. No improvement to the technology is evident. Therefore, the additional elements, alone or in combination, do not integrate the abstract idea into a practical application.
Step 2B of the subject matter eligibility test (see MPEP 2106.05).
Claims 1 and 5 do not include additional elements, alone or in combination, that are sufficient to amount to significantly more than the judicial exception (i.e., an inventive concept) for the same reasons as described above.
Therefore the claims do not appear to comprise limitations that integrate the exception into a practical application nor amount to significantly more than the above-judicial exception (the abstract idea). Looking at the limitations as an ordered combination (that is, as a whole) adds nothing that is not already present when looking at the elements individually. There is no indication that the combination of elements improves the functioning of a computer, for example, or improves any other technology. There is no indication that the combination of elements permits automation of specific tasks that previously could not be automated. There is no indication that the combination of elements includes a particular solution to a computer-based problem or a particular way to achieve a desired computer-based outcome.
Analysis of the dependent claims:
Claims 2-4 and 6-11 depend from the independent claims. Claims 2 and 6-7 recite additional abstract steps of training the model using a plurality of training sets that respectively correspond to a plurality of training protein complexes, each of the training complexes including at least one pair of the training residues. The additional abstract step recited at such a high level of generality does not require any specifically undue complexity that cannot be performed with pen and paper by a person of ordinary skill in the art. Therefore, the additional step of training the model is considered part of the JE and does not either integrate the JE into a practical application nor add significantly to the JE.
The dependent claims 3-4 and 8-11 merely further define the abstract idea and are, therefore, directed to an abstract idea for similar reasons: they merely describe additional details of calculations. Therefore, the additional limitations are not considered to integrate the JE into a practice application nor add significantly to the JE itself.
Response to Arguments
Applicant's arguments filed 4/30/2026 have been fully considered but they are not persuasive.
Applicant argues that the amended claims to comprise mutant protein complex comprising a mutant spike protein, which has a minimum number of amino acids (e.g. 1200 to 1400) and therefore cannot be practically performed in the mind.
Applicant arguments are not found persuasive. As applicant has acknowledged in their arguments, the claims are directed to a series of calculation steps resulting in a data value that one of ordinary skill in the art would understand how to perform. Although the amended language may now require more calculations due to a generally larger number of amino acids being present (e.g. 1200-1400), the sequence of calculation steps remain the same and therefore continue to read on steps that can be performed in the mind and/or limitations that just read on mathematical calculations.
Applicant further argues that the claimed invention provides a novel computing invention for estimating the binding of free energy without conducting biochemical experimentation and provides technical advancement in the field.
Applicant argument is not found persuasive as it appears to be directed solely to the identified JE itself, wherein the improvement should not solely reside within the JE. Essentially the argument appears to be directed towards an attempt at patenting better math. Applicant’s argument directed towards a technical improvement does not appear commensurate in scope with the claimed invention. There does not appear to be supportive documentation that necessitates the claimed sequence of mathematical steps results in a technical improvement, just an alternative method for arriving at an estimation of binding free energy. As such the arguments have not been found persuasive and the rejection is being maintained.
Conclusion
No claim is 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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jason Sims, whose telephone number is (571)-272-7540.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s supervisor, Jonathan Moffat can be reached via telephone (571)-272-4390.
Papers related to this application may be submitted to Technical Center 1600 by facsimile transmission. Papers should be faxed to Technical Center 1600 via the Central PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993) (See 37 CFR § 1.6(d)). The Central PTO Fax Center number is (571)-273-8300.
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/JASON M SIMS/Supervisory Patent Examiner, Art Unit 3791
Prosecution Insights