DETAILED ACTION
The Applicant’s response, received 05 March 2026, has 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.
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 .
Status of the Claims
The claim set received 05 March 2026 shows claim 21 with a status indicator of “Original” however the previous claim set received 23 July 2025 shows claim 21 with a status indicator of “Canceled.”
The claim set received 05 March 2026 does not include claim 31, which had a status indicator of “New” in the previous claim set received 23 July 2025 (i.e., page 13 is not in the claim amendment, and the filing does not contain a page 13 elsewhere).
In view of the above-mentioned issues regarding claims 21 and 31 in the presently filed claim set, the claims filed 05 March 2026 are non-compliant with 37 C.F.R. 1.121 because of the following omission(s) or matter(s): The claim text does not include necessary markings required by 37 C.F.R. 1.121 such as, status identifiers (e.g., “currently amended” or “original”); or markings to indicate the changes that have been made relative to the immediate prior version of the claims (23 July 2025).
However, instead of mailing a notice of non-compliance, the amendment received 05 March 2026 is entered and examined herein, as noted below, with claim 21 treated as having been canceled and claim 31 treated as pending and unamended (i.e., as filed in the claim set received 23 July 2025). If the Applicant wants the embodiments of canceled claim 21, then those embodiments would have to be added as new claim 32.
Claims 1-4, 7-20 and 22-31 are pending.
Claims 1-4, 7-20 and 22-31 are rejected.
Claims 4, 10, 11, 21, and 24 are objected to.
Priority
This application is a CON of PCT/US2024/012903, filed 25 January 2024, which claims benefit of 63/481, 776, filed 26 January 2023;
and claims benefit of 63/501,107, filed 09 May 2023;
and claims benefit of 63/589,207, filed 10 October 2023.
Claims 1-4, 7-20 and 22-31 are given the benefit of 63/481; 63/501,107; and 63/589,207.
Therefore, the effective filing date of the claimed invention is 26 January 2023.
Information Disclosure Statement
The information disclosure statement (IDS) received 05 March 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Drawings
The replacement drawings received 05 March 2026 are not accepted, and are objected to because the file submitted with the amendment does not actually include any replacement figures.
Therefore, the objection to the drawings in the Office action mailed 05 December is maintained, and reiterated below.
The replacement drawings received 08 October 2025, have not addressed the issues of record, and are objected to as noted below.
The drawings are objected to because separate views are not labeled with a number followed with a capital letter as required by 37 C.F.R. 1.84(u)(1) (see MPEP 608.02 V.).
In particular:
Fig. 9B (Cont’d.) at sheet 13/18 is not labeled in accordance with 37 C.F.R. 1.84(u)(1), and should be relabeled appropriately, with all subsequent figures relabeled accordingly, if necessary;
Fig. 9B (Cont’d.) at sheet 14/18 is not labeled in accordance with 37 C.F.R. 1.84(u)(1), and should be relabeled appropriately, with all subsequent figures relabeled accordingly, if necessary; and
Fig. 9B (Cont’d.) at sheet 15/18 is not labeled in accordance with 37 C.F.R. 1.84(u)(1), and should be relabeled appropriately, with all subsequent figures relabeled accordingly, if necessary.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The amendment to the Specification received 05 March 2026 has been entered.
Claim Interpretation
Claims 1, 29, and 30 recite the limitation “receiving an input protein molecule, wherein the input sequence includes….” This limitation is interpreted to mean a data representation of a protein molecule is being received.
Claims 1, 8, 9, 11, 12, 13, 15, 17, 19, 29, and 30 recite the limitation “input three-dimensional structure.” The broadest reasonable interpretation of this limitation is a data file containing data for encoding the three-dimensional structure (e.g., atomic coordinates (i.e., the precise x, y, z location of each atom); connectivity (i.e., which atoms are bonded to which); and secondary structure information).
Claim Objections
The objections to claims 1, 14, and 19 in the Office action mailed 05 December 2025 are withdrawn in view of the amendment received 05 March 2026.
The objection to claim 24 in the Office action mailed 05 December 2025 is maintained in view of the amendment received 05 March 2026, and reiterated below.
Claim 24 is objected to because of the following informalities: The word “to” between the word “generated” and the word “by” in line two should be deleted.
Appropriate correction is required.
The amendment received 05 March 2026 has been fully considered, however after further consideration, new grounds of objection are raised in view of the amendment, as noted below.
Claim 4 is objected to because of the following informalities: The word “a” in line two should be deleted.
Claims 10 and 11 are objected to because of the following informalities: The claims do not comply with 37 C.F.R. 1.121 (c), as noted below.
All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of "currently amended," and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims.
Claim 21 is objected to because of the following informalities: The claims do not comply with 37 C.F.R. 1.121 (c), as noted below.
The claim status indicator of the present claim is “Original” however the status indicator of the immediate prior version of the claim was “Canceled.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The rejection of claims 1-13, 15-20 and 22-31 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 05 December 2025 is withdrawn in view of the amendment received 05 March 2026.
The amendment received 05 March 2026 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 112(b) in view of the 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 1-4, 7-20 and 22-31 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. ii
Claim 1 recites the limitation “the input three-dimensional structure” in line seven. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-4, 7-20 and 22-28 are indefinite for depending from claim 1 and for failing to remedy the indefiniteness of claim 1.
Claim 29 recites the limitation “the input three-dimensional structure” in line four. There is insufficient antecedent basis for this limitation in the claim.
Claim 30 recites the limitation “the input three-dimensional structure” in line six. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 101
The amendment received 05 March 2026 has been fully considered, however after further consideration, the rejection of claims 1-13, 15-20, and 22-31 are rejected under 35 U.S.C. 101 in the Office action mailed 05 December 2025 has been maintained with modification in view of the amendment, as noted below.
The rejection of claims 5 and 6 has been withdrawn in view of these claims having been cancelled in the amendment received 05 March 2026.
Claim 14 has been rejected under 35 U.S.C. 101 in view of the amendment received 05 March 2026, as noted below.
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 1-4, 7-20, and 22-31 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-4, 7-20, 22-28, and 31 recite a system comprising at least one data processor and at least one memory (i.e., a machine or manufacture); claim 29 recites a computer-implemented method (i.e., a process); and claim 30 recites a non-transitory computer readable medium (i.e., a machine or manufacture).
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claims 1, 29, and 30 recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
generating a representation of the input protein molecule including the input sequence and the input three-dimensional structure (i.e., mental processes and mathematical concepts),
wherein the representation of the input protein molecule comprises a fixed size matrix including, for each residue in the input sequence, (i) a residue type and (ii) the atomic position of one or more constituent atoms (i.e., mental processes),
wherein the fixed size matrix is generated by at least assigning, to each residue in the input sequence, a structural role from a fixed set of structural roles (i.e., mental processes), and
wherein the representation of the input protein molecule includes a gap character in any position in the input sequence where the input sequence lacks a residue having a corresponding structural role (i.e., mental processes); and
applying a protein design computation model to jointly denoise the input sequence and the input three-dimensional structure by at least modifying the fixed size matrix (i.e., mathematical concepts), wherein
the modifying includes (i) inserting a new residue into the input sequence by replacing an existing gap character with the new residue and/or (ii) deleting an existing residue by replacing the existing residue with a new gap character such that a length of the input sequence is changed without changing one or more dimensions of the fixed size matrix (i.e., mental processes); and
generating, based at least on the modified fixed size matrix, an output sequence and an output three-dimensional structure comprising an output protein molecule having one or more drug-like properties (i.e., mathematical concepts).
Dependent claims 2-4, 7-20, 22-28, and 31 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
the fixed size matrix includes a plurality of rows, and wherein each row of the plurality of rows corresponds to a position in the input sequence (i.e., mental processes and mathematical concepts).
Dependent claim 3 further recites:
the fixed size matrix includes one column populated by an encoding of the residue type of each residue in the input sequence, and wherein the matrix further includes, for each possible atom forming a residue, a column populated by one or more coordinates defining the atomic position of the atom (i.e., mental processes and mathematical concepts).
Dependent claim 4 further recites:
the quantity of rows and/or a quantity of columns present in the fixed size matrix remain the same when the modifying of the fixed size matrix changes the length of the input sequence (i.e., mental processes and mathematical concepts).
Dependent claim 7 further recites:
generating the representation of the input protein molecule by at least determining, based at least on a position of each atom in one or more residues adjacent to a gap character, a position of one or more nonexistent atoms associated with the gap character (i.e., mental processes and mathematical concepts).
Dependent claim 8 further recites:
the protein design computation model jointly denoises the input sequence and the input three-dimensional structure over a plurality of successive denoising steps (i.e., mathematical concepts).
Dependent claim 9 further recites:
the protein design computation model jointly denoises the input sequence and the input three-dimensional structure by at least removing a first portion of noise at a first step before removing a second portion of noise at a second step (i.e., mathematical concepts).
Dependent claim 10 further recites:
the protein design computation model generates the sequence of the output molecule to be invariant to special Euclidean group SE(3) transformations and the three-dimensional structure of the output molecule to be equivariant to special Euclidean group SE(3) transformations (i.e., mathematical concepts).
Dependent claim 11 further recites:
the protein design computation model jointly denoises a plurality of frames in which each frame corresponds to the input three-dimensional structure being oriented in one direction along a principal axis of rotation about a centroid of the input three-dimensional structure, and wherein the protein design computation model generates the three-dimensional structure of the output molecule by at least averaging a result of jointly denoising the plurality of frames (i.e., mathematical concepts).
Dependent claim 12 further recites:
the plurality of frames includes a first frame in which the input three-dimensional structure is oriented in one direction along a first principal axis of rotation, a second frame in which the input three-dimensional structure is oriented in an opposite direction along the first principal axis of rotation, a third frame in which the input three-dimensional structure is oriented in one direction along a second principal axis of rotation, and a fourth frame in which the input three-dimensional structure is oriented in the opposite direction along the second principal axis of rotation (i.e., mental processes and mathematical concepts).
Dependent claim 13 further recites:
the protein design computation model determines, based at least on a direction of the input three-dimensional structure along the first principal axis of rotation and a direction of the input three-dimensional structure along the second principal axis of rotation, a direction of the input three-dimensional structure along a third principal axis of rotation (i.e., mathematical concepts).
Dependent claim 14 further recites:
the protein design computation model includes a plurality of blocks, wherein each block of the protein design computation model includes one or more multilayer perceptrons (MLP), and wherein the plurality of blocks are applied consecutively to the representation of the input protein molecule (i.e., mathematical concepts).
Dependent claim 15 further recites:
the protein design computation model includes a projection layer that modifies, based on one or more bond constraints, the input three-dimensional structure (i.e., mathematical concepts).
Dependent claim 16 further recites:
the one or more bond constraints are imposed based on a reference residue backbone comprising a plurality of rigid atoms with fixed bond lengths and fixed bond angles (i.e., mathematical concepts).
Dependent claim 17 further recites:
the projection layer modifies the input three-dimensional structure by at least determining one or more transformations that minimize a distance between the plurality of rigid atoms in the reference residue backbone and one or more backbone atoms in the input three-dimensional structure (i.e., mathematical concepts), and
applying the one or more transformations to align the input three-dimensional structure to the reference residue backbone (i.e., mathematical concepts).
Dependent claim 18 further recites:
the protein design computation model jointly denoises, for each residue of the plurality of residues in the input sequence, a generic sidechain comprising pseudo atoms having a same degrees of freedom as sidechain atoms in an actual residue (i.e., mathematical concepts).
Dependent claim 19 further recites:
the projection layer modifies the input three-dimensional structure subsequent to the joint denoising by the protein design computation model by at least applying a dihedral angle between one or more pseudo atoms in the generic sidechain to a sidechain template specifying an idealized dihedral angle between one or more sidechain atoms of a corresponding type of residue (i.e., mathematical concepts).
Dependent claim 20 further recites:
determining prior data distribution corresponding to a generative task of generating one or more protein molecules from a specific protein family (i.e., mathematical concepts); and
incorporating the prior data distribution by at least generating, based at least on the prior data distribution, one or more training samples for the protein design computation model (i.e., mathematical concepts).
Dependent claim 22 further recites:
the prior data distribution includes a positional residue frequency specifying a likelihood of different types of residues occupying each position in a protein sequence (i.e., mathematical concepts).
Dependent claim 23 further recites:
the prior data distribution includes a conditional atom dependency specifying a relative position of atoms in adjacent residues (i.e., mathematical concepts).
Dependent claim 24 further recites:
the one or more training samples are generated by at least adding, to one or more training protein molecules, noise sampled from the prior data distribution (i.e., mathematical concepts).
Dependent claim 25 further recites:
the noise includes one or more modifications to at least one of a residue type and atomic positions (i.e., mathematical concepts).
Dependent claim 26 further recites:
the one or more training samples are generated by a forward diffusion process that includes an incremental addition of the noise sampled from the prior data distribution (i.e., mathematical concepts).
Dependent claim 27 further recites:
the protein design computation model generates the output protein molecule to exhibit a same drug-like property as the input protein molecule, a different drug-like property as the input protein molecule, and/or to modify a magnitude of a drug-like property present in the output protein molecule (i.e., mathematical concepts).
Dependent claim 28 further recites:
the one or more drug-like properties include expression, binding affinity towards a target molecule, specificity, stability, non-immunogenicity, human-ness, and/or lack of self-association (i.e., mental processes).
Dependent claim 31 further recites:
generating the output protein molecule comprises generating a sequence of the output protein molecule or a three-dimensional structure of the output protein molecule (i.e., mathematical concepts).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., generating the representation (e.g., a data matrix) by assigning values to protein characteristics and populating a matrix with the values), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., generating a representation (e.g., a matrix) involves creating an array of numerical values that represent physical characteristics and are arranged in rows and columns (e.g., an m × n matrix)); using the protein design computation model involves performing mathematical operations on the matrix (i.e., the generated representation); and using the model to perform denoising of the input sequence and the input three-dimensional structure is a mathematical process that requires calculations using particular equations (e.g., ¶¶ [0083] & [0093] in the Specification)) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-4, 7-20, and 22-31 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 2-4, 7-20, 22-28, and 31 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
at least one data processor;
at least one memory storing instructions; and
an input protein molecule, wherein the input sequence includes a plurality of residues, and wherein the input three-dimensional structure includes an atomic position of one or more atoms forming each residue included in the input sequence (i.e., receiving data).
The additional elements in independent claim 29 include:
receiving an input protein molecule, wherein the input sequence includes a plurality of residues, and wherein the input three-dimensional structure includes an atomic position of one or more atoms forming each residue included in the input sequence (i.e., receiving data).
The additional elements in independent claim 30 include:
a non-transitory computer readable medium storing instructions;
at least one data processor; and
receiving an input protein molecule, wherein the input sequence includes a plurality of residues, and wherein the input three-dimensional structure includes an atomic position of one or more atoms forming each residue included in the input sequence (i.e., receiving data).
The additional elements of at least one data processor (claims 1 and 30); at least one memory storing instructions (claim 1); and a non-transitory computer readable medium storing instructions (claim 30); invoke a computer and/or computer-related components merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d)(1)).
The additional element of receiving an input protein molecule, wherein the input sequence includes a plurality of residues, and wherein the input three-dimensional structure includes an atomic position of one or more atoms forming each residue included in the input sequence (i.e., receiving data) (claims 1, 29, and 30); is merely a pre-solution activity of gathering data for use in the claimed process – a nominal or tangential addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer and/or computer related components as tools; and/or amount to insignificant extra-solution activity; and as such, when all limitations in claims 1-4, 7-20, and 22-31 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-4, 7-20, and 22-31 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 2-4, 7-20, 22-28, and 31 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1, 29, and 30 are identified above, and carried over from Step 2A Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of at least one data processor (claims 1 and 30); at least one memory storing instructions (claim 1); a non-transitory computer readable medium storing instructions (claim 30); and receiving data (claims 1, 29, and 30); are conventional computer components and/or functions (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
Therefore, when taken alone, all additional elements in claims 1-4, 7-20, and 22-31 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-4, 7-20, and 22-31 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 05 March 2026 have been fully considered, but are not persuasive.
The Applicant provides arguments against the rejection under 35 U.S.C. 101 on pages 14-16 of the Remarks, and states on page 14 (para. 4) that the present amendments obviate the rejections under 35 U.S.C. 101. On pages 14-15 of the Remarks the Applicant points to the “2024 Guidance Update on Patent Subject Matter Eligibility, Including on Artificial Intelligence” (hereinafter, “Guidance”) and the Applicant further references the Guidance’s analysis of McRO, and states on page 15 (para. 2) that akin to McRO, instant claim 1 recites specific details for realizing, through a protein design computation model operating on a fixed size representation of the sequence and structure of a protein molecule, a technological improvement to conventional approaches to computational protein design.
These arguments are not persuasive, because first, the present amendments do not obviate the rejections under 35 U.S.C. 101 for the reasons noted and discussed in the above rejection. Second, with regard to the Applicant’s attempt to analogize the instant claims with the eligibility determination in McRO, it is noted that in McRO, when looked at as a whole, claim 1 is directed to a patentable, technological improvement over the existing, manual 3-D animation techniques, i.e., the claim recited “a specific asserted improvement in computer animation” that was directed to the creation of something physical – namely, the display of lip synchronization and facial expressions of animated characters on screens for viewing by human eyes, and therefore was determined to not be directed to an unpatentable abstract idea at Eligibility Step 2A (i.e., Alice step one). Unlike the technological improvement found in McRO, the instant claimed advantage of realizing, through a protein design computation model operating on a fixed size representation of the sequence and structure of a protein molecule, to achieve the claimed technological improvement to computational protein design, is a purported improvement to the abstract idea (data analysis), and not an improvement to computer functionality itself, or an improvement to another technology or technical field.
The Applicant states on page 15 (para. 3) that the subject matter of instant claim 1 is also patent eligible under Ex Parte Desjardins, (hereinafter, “Desjardins”). The Applicant further states that under Desjardins, improvements to a computation model itself can be sufficient for the purpose of patent eligibility, even if an abstract idea is otherwise claimed. The Applicant further states that the subject matter of instant claim 1 includes a fixed sized representation of the input protein molecule that improves the computational efficiency of the claimed protein design computation model by enabling the protein design computation model to accommodate length changes to the sequence of the input protein molecule without any increase in architectural complexity of the protein design computation model, and that, for example, as set forth in claim 1, “the representation of the input protein molecule includes a gap character in any position in the input sequence where the input sequence lacks a residue having a corresponding structural role” and the claimed protein design computation model modifies the representation of the input protein molecule to generate an output protein molecule by at least “(i) inserting a new residue into the input sequence by replacing an existing gap character with the new residue and/or (ii) deleting an existing residue by replacing the existing residue with a new gap character such that a length of the input sequence is changed without changing one or more dimensions of the fixed size matrix.” The Applicant points to paragraph [0057] in the specification, and further states on page 16 (bottom) that in addition, the subject matter o the claim is also subject matter eligible under Enfish, and according to Enfish, “[t]he fact that a claim is directed to an improvement in computer-related technology can demonstrate that the claim does not recite a concept similar to previously identified abstract ideas.” The Applicant points to paragraphs [0052] – [0053] in the specification, and further states (pages 16-17) that, akin to Enfish, instant claim 1 describes a specific way to solve a technological problem of “a naïve design approach that relies on a brute force examination of every possible sequence and conformational variation [being] computationally intractable for protein sequences of meaningful length” and the suboptimal outcomes of “segregating sequence design and structural analysis may also yield suboptimal outcomes.” The Applicant further states on page 17 (para. 1) that applying the Enfish rationale, claim 1 does not recite an abstract idea at least because operating on a fixed size matrix during the generative process improves computational protein design by at least accommodating length changes to the sequence of the input protein molecule with less memory overhead. The Applicant further states that as noted, the present claims recite specific details on how the improvements in computer-related technology are realized, and (para. 2) for at least these reasons, the instant claims are not directed to an abstract idea.
These arguments are not persuasive, because first, with regard to the Applicant’s attempt to analogize the instant claims to the claims in Desjardins, these arguments are not persuasive at least because the fact patterns differ between the claims at issue in Desjardins and the instant claims, not least in that the “ARP” in Desjardins notes that the Federal Circuit held that the eligibility determination should turn on whether “the claims are directed to an improvement to computer functionality versus being directed to an abstract idea” (citing Enfish), prior to the “ARP” finding that the improvement to how the machine learning model operates allows artificial intelligence (AI) systems to use less of their storage capacity and enables reduced system complexity, as supported by the Specification – i.e., the improvement to the model provided an improvement to computer functionality itself. This fact pattern contrasts with the instant claim 1 fact pattern of a fixed sized representation of the input protein molecule that purportedly improves the computational efficiency of the claimed protein design computation model by enabling the protein design computation model to accommodate length changes to the sequence of the input protein molecule without any increase in architectural complexity of the protein design computation model. Second, regarding the Applicant’s attempt at analogizing the instant claims to Enfish, the instant claims are not analogous to the claims in Enfish, because the instant claims recite a computational model operating on a fixed size matrix during a generative process of protein design by at least accommodating length changes to the sequence of the input protein molecule with purportedly less memory overhead (i.e., memory usage versus a reconfigured memory), whereas in contrast, the improvement recited in Enfish is found in a data structure that corresponds to a storage and retrieval structure configured in a computer memory comprising a self-referential table that is designed to improve the way a computer stores and retrieves data in memory, and thus is an improvement to computer functionality itself. Stated a different way, the improvement was found in the structure of the table itself (e.g., relationships between rows and columns), irrespective of any particular data being stored or searched.
Claim Rejections - 35 USC § 103
The rejection of claims 1-9, 15, 16, 17, 20, and 22-31 under 35 U.S.C. 103 as being unpatentable over Anand et al. in view of Hoogeboom et al. in the Office action mailed 05 December 2025 is withdrawn in view of the amendment received 05 March 2026.
The rejection of claim 10 under 35 U.S.C. 103 as being unpatentable over Anand et al. in view of Hoogeboom et al. as applied to claims 1-9, 15, 16, 17, 20, and 22-31 above, and further in view of Qiao et al. in the Office action mailed 05 December 2025 is withdrawn in view of the amendment received 05 March 2026.
The rejection of claims 11, 12, and 13 under 35 U.S.C. 103 as being unpatentable over Anand et al. in view of Hoogeboom et al. as applied to claims 1-9, 15, 16, 17, 20, and 22-31 above, and further in view of Puny et al. in the Office action mailed 05 December 2025 is withdrawn in view of the amendment received 05 March 2026.
The rejection of claims 18 and 19 under 35 U.S.C. 103 as being unpatentable over Anand et al. in view of Hoogeboom et al. as applied to claims 1-9, 15-16, 17, 20, and 22-31 above, and further in view of Koga et al. in the Office action mailed 05 December 2025 is withdrawn in view of the amendment received 05 March 2026.
Response to Arguments
The Applicant’s arguments/remarks received 05 March 2026 have been fully considered, and are persuasive.
The Applicant provides arguments/remarks (Remarks, pages 17-20) traversing the rejections under 35 U.S.C. 103 in the Office action mailed 05 December 2025, and states that the amendments to claim 1 further clarify the claimed subject matter, such that the cited references do not disclose or suggest a “fixed size matrix” or a “protein design computation model modifying a fixed size matrix” according to the amended claim limitations.
These arguments are persuasive.
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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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687
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