DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
17-18, 20-22, 27, 29-30, 34-35, 39-40
Pending:
1-16, 19, 23-26, 28, 31-33, 36-38 and 41-43
Withdrawn:
8-9, 31-33, 36-38 and 42
Examined:
1-7, 10-16, 19, 23-26, 28, 41 and 43
Independent:
1 and 41
Allowable:
none
Rejections applied
Abbreviations
x
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
102, 103
JE
Judicial Exception
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
x
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 8/1/2025 filing receipt, this application claims priority to as early as 1/17/2023. At this point in examination, all claims have been interpreted as being accorded this priority date.
Moving toward allowance...
It would simplify the final steps toward rejoinder and allowance if the withdrawn claims were amended where appropriate to reflect amendments already made to the examined claims.
Withdrawal / revision of objections and/or rejections
In view of the amendment and remarks:
The previous objections to the claims are withdrawn.
The 112/b rejections are withdrawn, except as noted.
The 103 rejections are withdrawn. The claims are free of the analogous art at least because close art, e.g. as cited in the now withdrawn rejection as well as art found in the search histories, either individually or in obvious combination, does not teach the recited, for example claim 1, combination of determining, within input sequence, an adjustable segment and a fixed segment, wherein the fixed segment is associated with one or more properties of interest; modifying the input sequence by at least applying a protein design computation model trained to approximate a distribution of protein sequences exhibiting a first property, wherein the protein design computation model modifies the input sequence by at least: applying an energy-based model (EBM) to modify the adjustable segment of the input sequence. Additionally, Applicant's 2/5/2026 remarks at pp. 20-21 supported the withdrawal of the rejection.
The 101 rejections are withdrawn. Referring to 101 analysis as organized in MPEP 2106, the 101 rejections are withdrawn at least in view of the analysis Step 2A, 2nd prong, 1st consideration relating to an improvement over the previous state of the technology field integrating possible judicial exceptions into a practical application (MPEP 2106.04(d) and (d)(1)), the improvement in this instance comprising decrease in required computational resources and increase in likelihood of utility of proteins for therapy. In this regard, Applicant's 2/5/2026 remarks at pp. 16-18 support withdrawal of the rejection.
Rejections and/or objections not maintained from previous office actions are withdrawn. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim rejections - 112/b
The following is a quotation of 35 USC 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.
Claims 1-7, 10-16, 19, 23-26, 28 and 43 are rejected under 112/b, as indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate, including in withdrawn claims. With regard to any suggested amendment below, for claim interpretation during the present examination it is assumed that each amendment suggested here is made. However equivalent amendments also would be acceptable.
The following issues cause the respective claims to be rejected under 112/b as indefinite:
Claim
Recitation
Comment (suggestions in bold)
1
at least one memory storing instructions which, when executed by the at least one data
processor, result in operations comprising:
Claim 1 is rejected as directly reciting a machine and a process in the same claim. A claim to a machine, e.g. here a "system," cannot directly recite a process step such as "result." MPEP 2173.05(p).II pertains. It may suffice to add "configured to" before the process step so as properly focus on claimed structure. MPEP 2173.05(p).II pertains regarding a claim directed to both product and process.
This rejection is maintained.
6, 16
...is trained...
Ambiguous as to whether the recited present tense training is a required, software-embodied process step of the system claim or, as in the "...model trained..." of claim 1, further reads on product-by-process (PbP). It is unclear when the training is required to occur or to have occurred.
In claims 1 and 41, the recited "...model trained..." is interpreted as a PbP element, i.e. the recited "model..." limited according to any structure clearly required by the recited PbP limitation of having been "trained..." The recited process or step of having been "trained" is not itself claimed and is limiting only to the extent that the structure of the "model" is clearly required to be limited by that process or step. Regarding PbP limitations within a claim, MPEP 2113 pertains, as well as, for example, Biogen MA, Inc. v. EMD Serono, Inc. (Fed. Cir. 9-28-2020, precedential).
This contrasts with claim 23 which clearly requires a "training" step.
Claim 16 is rejected similarly.
This rejection might be overcome, for example, by amending to "was trained" if PbP is intended or by amending to "training" (with appropriate associated grammatical amendments) if PbP is not intended.
This rejection is maintained.
7
an energy function
The relationship is unclear between this instance and that in claim 1.
Possibly "first" and "second" energy functions should be recited.
This rejection is maintained.
7
a likelihood of a sequence
The relationship is unclear between this instance and that in claim 1, 2nd "applying" step.
Possibly "first" and "second" likelihoods should be recited.
This rejection is maintained.
Nonstatutory double patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine to prevent the improper timewise extension of the "right to exclude" granted by a patent and to prevent multiple suits against an accused infringer by different assignees of the same invention (MPEP 804.II.B, 1st para.). A nonstatutory double patenting rejection is appropriate where the conflicting claims (instant v. reference) are not identical, but an examined-application claim (instant claim) is not patentably distinct from a reference claim because the instant claim is either anticipated by, or would have been obvious over, the reference claim (MPEP 804.II.B, 2nd para.).
In cases of double patenting rejections versus reference claims of pending applications, as opposed to claims of an issued patent, the rejections are provisional because the reference claims have not been patented. Presently, no rejections are provisional.
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the application or patent of the reference claim either is shown to be commonly owned with the instant application or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. A registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must comply fully with 37 CFR 3.73(b).
Applicant may wish to consider electronically filing a terminal disclaimer (MPEP 1490.V pertains, along with https://www.uspto.gov/patents-application-process/applying-online/eterminal-disclaimer). Electronic filing may lead to faster approval of the disclaimer. Also, if filing electronically, Applicant is encouraged to notify the examiner by telephone so that examination may resume more quickly.
Double patenting rejections of instant claims 1-7, 10-16, 19, 23-26, 28, 41 and 43
Instant claims 1-7, 10-16, 19, 23-26, 28, 41 and 43 are rejected on the grounds of nonstatutory double patenting as unpatentable over one or more claims in reference applications 19/216,541 and 19/278,505 in view of Tagasovska (as cited on the 7/17/2025 IDS).
Although the reference claims are not identical to the instant claims, in a BRI they also are not patentably distinct from the instant claims: either (i) because the instant claims recite obviously equivalent or broader limitations in comparison to the reference claims or (ii) because the instant claims recite limitations which are obvious over the cited art. It is not clear that the instant claims recite limitations which are narrower than limitations in the reference claims.
Each reference patent and application recites claims which involve using a molecular design computation model to analytically modify molecular structure. The instantly recited generating a modified sequence would have been prima facie obvious in view of the reference application in combination with the cited art.
It would have been obvious in view of the cited art to modify reference claims to arrive at the rejected instant claims. Either the instant limitations are interpreted as reading on a reference limitation, or the instant limitations would have been obvious in view of the cited art. That is, to the extent that any instant claims are narrower than reference claims, then any such narrowing would have been obvious over the cited art.
Conclusion
No claim is allowed.
Applicant's amendments necessitated the new grounds for rejection in this 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.
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The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs, II, may be reached at (571) 270-3062.
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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