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 .
The present application is a Track One Request granted 07 March 2024.
Status of the Claims
Claim set received 02 February 2026 has been entered into the application.
Claim 1-2, 5-6, 9, and 16-20 are amended.
Claims 10, 14, and 21 are cancelled.
Claim(s) 1-9, 11-13, and 15-20 are pending.
Priority
This Application is a continuation US Patent Application 18/513,867 filed 20 November 2023 which is a continuation of and claims priority to PCT/IB202/054705 filed 19 May 2022 which claims further benefit to European Application 21382464.2 filed 21 May 2021.
Specification
The objection to the specification in the Office Action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026.
Claim Rejections - 35 USC § 112
USC § 112(a)
New Matter
The rejection of claim 1 under 35 U.S.C § 112(a) in the Office action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026.
Written Description
The rejection of claim 1 under 35 U.S.C § 112(a) in the Office action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026.
USC § 112(b)
The rejection of claim 1-9, 11-13, and 15-20 under 35 U.S.C § 112(b) in the Office action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026.
The rejection of claim 10, 14, and 21 under 35 U.S.C § 112(b) in the Office action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026 because the claims are cancelled.
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reason for record in the Office Action mailed 02 October 2025 and modified in view of the amendments filed 02 February 2026. It is noted the amendments received 02 February 2026 are necessitated by new ground(s) of rejection.
The rejection of claim 10, 14, and 21 under 35 U.S.C § 101 in the Office action mailed 02 October 2025 is withdrawn in view of the amendments filed 02 February 2026 because the claims are cancelled.
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 1-9, 11-13, and 15-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claim Analysis
Under broadest reasonable interpretation (BRI), the claims encompass utilizing computer limitations because claim 1 recites “in silico for generating polypeptide structures” which requires computer process, component, and equipment.
Following the flowchart of the MPEP 2106
Step I - Process, Machine, Manufacture or Composition
Claims 1-9, 11-13, and 15-20 are directed towards a method, so a process.
2A Prong I- Step 2A Prong One: Identification of an Abstract Idea
Claims 1 recites
(a) providing a polypeptide sequence of the target polypeptide
This step can be performed in the human mind by following instructions to provide a target polypeptide sequence data and is therefore an abstract idea.
(b) performing a molecular dynamic (MD) simulation to model conformational dynamics of the polypeptide sequence to obtain structural conformations on a computer system to generate output data (i.e., residue specific property and pairwise properties derived from MD simulations) with a plurality of continuous time frames, wherein the output data or each time frame comprises: (i) at least one residue-specific property derived from the MD simulation for an amino acid in the polypeptide, (ii) at least one pairwise property derived from the MD simulation for at least two amino acids in the polypeptide
This step encompasses performing mathematical computations of Molecular Dynamics simulations to generate output data (i.e., quantitative data/numerical value/variables (i.e., output data (i.e., residue specific property and pairwise properties derived from MD simulations))) which encompasses using mathematical/statistical formulas such as Newton’s Second Law, forces from potential energy, force fields, pairwise calculations, and time-integration which reads on abstract ideas. See MPEP 2106.04(a)(2)(I)(A)(iv). Here, it is noted step (i-ii) of claim 1 step (b) describes the output for time frames. It is also noted that steps (i-ii) of claim 1 step (b) read on mathematical variables as the subsequent step utilizes/arranges the properties into the dynamic graph function which also reads on abstract ideas.
(c) arranging the output data for each time frame among the plurality of continuous time frames into the at least one graph function, wherein the at least one graph function comprises dynamic graph function.
This step can be performed in the human mind by organizing data (i.e., output data related to continuous time frames) into a graph function (i.e., mathematical formula) and is therefore an abstract idea. This step encompasses arranging information (i.e., output data) into a mathematical formula/function (i.e., graph function [Spec page 20 para 64-65]) which reads on abstract ideas. This step encompasses graph function comprises continuous graph function comprising a dynamic graph function which reads on mathematical formula/function which reads on abstract ideas.
(d) encoding the at least one graph function into a dense vector embedding
This step can be performed can be performed in the human mind by organizing data (i.e., graph function) into dense vector embeddings [specification page 10 para 36, page 20 para 64-65] which reads on abstract ideas. This step encompasses taking information (i.e., output data (i.e., residue specific property and pairwise properties) and dynamic graph function), manipulating the data via mathematical function/correlation (i.e., encoding), and organizing the information into a different form (i.e., dense vector embeddings). See MPEP 2106.04(a)(2)(I)(A)(iv).
(3) applying a machine learning framework to the dense vector embedding, wherein the machine learning framework is trained to generate a predicted polypeptide structure target structure.
Here, even though the claimed steps apply a “machine learning framework”, the machine learning framework (MLF) is broadly and generically recited and reads on mere instructions to implement an abstract idea on a generic computer and reads on mathematical/statistical computations (i.e., linear region, bootstrap aggregation [Spec pages 10-11 para 39]). See 2024 Subject Matter Eligibility Update (AI) [Example 47 Claim 2] and MPEP 2106.04(a)(2)(III)(C)(1-3) and 2106.05(f). Furthermore, it is noted that the claimed step recites “to generate an in-silico polypeptide structure”. Here, the “…to generate a predicted polypeptide structure target polypeptide” of claim 1 step (e) is interpreted as generating information (i.e., organized amino acid sequence data) and not physical steps for generating a physical polypeptide.
40. Claims 2-9, 11-13, 15-20 are further drawn to limitations that describe the abstract ideas of claim 1 and are therefore also abstract ideas.
2A Prong II - Consideration of Practical Application
Claim 1 does not recite an additional element that integrates the recited judicial exception into a practical application.
Here, in the instant case, the claims merely set forth a method of data analysis yielding an in-silico generated polypeptide using a machine learning algorithm. Moreover, it is noted in Step 2A Prong I above, the “generated in-silico polypeptide structure” of claim 1 is interpreted as information (i.e., organized amino acid sequence data) and not physical steps for generating a physical polypeptide. Thus, the results of claim 1 only produce information (i.e., organized nucleic acid data (predicted polypeptide structure target polypeptide)) which does not provide for a practical application in the physical-realm of physical things and acts, i.e., the claims do not utilize the data generated by the judicial exception to affect any type of change. See MPEP 2106.04(a)(2)(I)(A)(iv).
Furthermore, and for sake of compact prosecution, even if the machine learning framework (MLF) is also considered additional elements, the MLF are used to generally apply the abstract idea without limiting how the trained (MLF) functions. The MLF is described at a high level such that it amounts to using a computer with a generic MLF to apply the abstract idea. These limitations only recite the outcomes for “applying a machine learning algorithm to a dense vector map to generate the polypeptide structure target polypeptide” without any details about how the target polypeptide is generated. Therefore, the judicial exception is not integrated into a practical application, and the claims do not provide significantly more because this type of recitation is equivalent to the words "apply it". See 2024 Subject Matter Eligibility Update (AI) [Example 47 Claim 2] and MPEP 2106.05(f).
With respect to claim 13, the claim recites “comprising selecting an intervention therapy based on the predicted polypeptide structure and the disease state”. Here, an intervention therapy is merely selected based on information (i.e., predicted polypeptide structure and the disease state) which reads on abstract ideas as noted in Step 2A Prong I of the 101 analyses above.
The judicial exception is not integrated into a practical application because the claims do not meet 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 claimed method also recites "additional elements" that are not limitations drawn to an abstract idea.
The recited additional elements of computer processes, components, equipment of claim 1 does not add significantly more than the recited judicial exception because using computer to perform abstract ideas is deemed well-understood, routine, and conventional. To exemplify the conventionality of using computers, Saadi teach using CTLPred, RANKPEP, mfold, Bcepred, and DiscTope 2.0 programs for predicting B-cell epitope and B-cell epitope structure [page 229 sections 2.2-2.13]. Saadi teach predicted structure of constructed protein using I-TASSER software [page 232 figure 5] (Infection, genetics and evolution, 2017-07, Vol.51, p.227-234) (Cited in the Office Action mailed 10/11/2024). To further exemplify the conventionality of using computers, Guerra teaches a schematic representation of the workflow to identify epitopes for vaccine development [page 406 fig 1] (Cited in the Office Action mailed 10/11/2024). To further exemplify the conventionality of using computers, Fleri teaches different prediction tools are available in the Analysis Resource with respect to different stages of MHC I antigen processing [page 6 fig 3] (Cited in the Office Action mailed 10/11/2024). To further exemplify the conventionality of using computers, Antonia teaches workflow of a typical IgE epitope localization project with SPADE as prediction tool [page 17 fig 6] (Methods (San Diego, Calif.), 2014-03, Vol.66 (1), p.3-21) (Cited in the Office Action mailed 10/11/2024).
The recited additional elements of data inputting of claim 11 does not add “significantly more” to the recited judicial exception because inputting data is deemed a well-understood and conventional extra-solution activity. See MPEP 2106.05(g).
In conclusion, and when 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 Arguments
Applicant's arguments filed 02 February 2026 have been fully considered but the rejection is maintained in view of the arguments received 02 February 2026.
The Applicant states the amended claims are directed towards a patent eligible subject matter. The Applicant points to the MPEP 2106 flowchart regarding the step of the eligibility analysis. The Applicant state the claims are patent eligible under Step 2A Prong I [remarks, page 8]. The Applicant points to the MPEP 2106.04(a)(2)(III)(A). The Applicant points to the example regarding the claimed method for rendering half-tone images. The Applicant states claim 1 cannot be performed in the human mind and points to the amendments to claim 1. The Applicant states MD simulations cannot be performed in the human mind [remarks, page 8]. The Applicant states one of ordinary skill would recognize that machine learning cannot be performed in the human mind. Thus, rendering the claims patent eligible. The Applicant states the amended claimed process cannot be performed in the human mind. The Applicant states the claims constitute a practical application in protein prediction. The Applicant points to Research Corporation Technologies, Inc. v. Microsoft Corp and McRo for guidance [remarks, page 9]. The Applicant states claim 1 cannot be performed in the human mind [remarks, page 9].
In response, as noted in Step 2A Prong I of the 35 U.S.C § 101 rejection above, claim 1 steps (a)-(e) can be performed in the human mind. For examples, step (a) is drawn to following instructions, (b) is drawn to performing mathematical computations (i.e., MD simulations) to generate quantitative data (i.e., residue-specific properties and pairwise properties), (c) is drawn to arranging/organizing, (d) is drawn to mathematically converting information (i.e., encoding) into dense vector embeddings, and (e) is drawn to analyzing polypeptide data/encodings (i.e., dense vector embeddings) via mathematical correlations/functions (i.e., machine learning framework) for predicting polypeptide structure target polypeptide which reads on abstract ideas. Furthermore, claim 1 step (b) encompasses using computer elements. Here, using a computer to perform in silico methods for polypeptide structural generation is merely performing mental processes/mathematical concepts on a generic computer, performing mental processes in a computer environment, and using a computer as a tool to perform the mental processes. See MPEP 2106.04(a)(2)(III)(C). It is noted that practical applicability is evaluated under Step 2A Prong II of the 101 analyses.
The Applicant states the claims are eligible under Step 2A Prong II of the 101 analyses. The Applicant states claim 1 is integrated into a practical application. The Applicant states the claims provide an improvement to technology. The Applicant points to the MPEP 2106.05(a)(II) [remarks, page 10]. The Applicant states the improvement is shorted simulation time. The Applicant points to specification paragraphs [17 and 37] for guidance [remarks, page 10]. The Applicant states the elements integrate the judicial exception into a practical application/improvement to technology. The Applicant states the specific technical feature improves functioning of a computer [remarks, page 11].
In response, and as noted in Step 2A Prong II of the 101 analyses above, claim 1 does not contain any additional elements that integrate the recited judicial exception into a practical application. With respect to paragraphs 17 and 37 of the specification providing an improvement to technology, the paragraphs merely provide statements that the claimed invention can provide shorten effective simulation time and allows for accurate prediction of structure beyond the current capabilities of molecular dynamics simulation. However, for example, the specification does not provide examples of comparison of other MD simulation capabilities, provide quantitative data illustrating shortened MD simulations and accuracy, and/or provide how the instant claimed invention provides “shortened effective simulation time and allows for accurate prediction of structure beyond the current capabilities of molecular dynamics simulation.” As such, the specification merely provides conclusory evidence/support (i.e., a bare assertion of an improvement without the detail necessary to be apparent to a person of ordinary skill in the art) for “shorten effective simulation time and allows for accurate prediction of structure beyond the current capabilities of molecular dynamics simulation.” which does not an improvement to a technology field or a practical application of the judicial exception. See MPEP 2106.04(d)(I) [second paragraph] and 2106.05(a) [third paragraph]. With respect to providing an improvement to a computer, the computer is not improved by the way of the claimed method as the claims, in light of the specification, do not set forth evidence that the claimed process causes a computer to operate differently than it ordinarily would. It appears that the claims are drawn to an abstract idea that may result in a computational process that is more efficient than others known in the art. However, the computer is not improved by way to the claimed process.
The Applicant states the claims are patent eligible under Step 2B of the 101 analyses. The Applicant states the claims contain an inventive concept and improves computer performance and computation structural biology. The Applicant points to MPEP 2106.05 for guidance. The Applicant states “generating dynamic graph for dense vector embedding as input of an artificial intelligence-based framework for structure”. The Applicant states generating dynamic graph functions is a specific mechanism, not a generic computing step. The applicant states the limitations improve the functioning of a computer. The Applicant states the method is applied to predicting polypeptide structures for drug discovery and protein engineering, a concrete technological field [remarks, page 11]. The Applicant states, under Step 2A Prong II, the rejection should be withdrawn.
It is noted claim 1 does not contain a “generating dynamic graph functions for dense vector embedding as input of an artificial intelligence-based framework for structure prediction” step. As noted in Step 2A Prong I of the 101 analyses above, the “generating” limitations are associated with mathematical concepts (i.e., MD simulations to generate output data, generate a predicted polypeptide structure) which read on abstract ideas. Here, “generating dynamic graph functions” would merely be performing mathematical computations for converting data into vectors which does not provide an inventive concept and reads on abstract ideas. See MPEP 2106.04(a)(2)(I)(A)(iv). Furthermore, the claims, in light of the specification, do not set forth evidence that “the claimed process causes a computer to operate differently than it ordinarily would. Thus, the computer is not improved by way to the claimed process and is merely utilized as a tool to perform the abstract ideas in a computing environment for computing efficiency. See MPEP 2106.04(a)(2)(III)(C) (1-2). Thus, under Step 2B of the 101 analyses, the claims do not contain an invention concept. Therefore, the claims are not patent eligible under 35 U.S.C § 101.
Double Patenting
Provisional Double Patenting
The rejection of claims 1, 7, and 21 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 13, 15-17, 21, and 26 of copending Application No. 18/598,694 (‘694) in the Office Action mailed 02 October 2025 is withdrawn in view of the amendments received 02 February 2026.
The rejection of claims 1-21 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 40-49 and 59 of copending Application No. 18/513, 867 (‘867) in the Office Action mailed 02 October 2025 is withdrawn in view of the amendments received 02 February 2026.
Objections
The instant objections are maintained for reason for record in the Office Action mailed 02 October 2025 and modified in view of the amendments filed 02 February 2026.
Applicant is advised that should claims 3-5 and 9 be found allowable, claim 20 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Applicant is advised that should claims 5 and 7 be found allowable, claim 16 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Applicant is advised that should claims 7 and 9 be found allowable, claim 19 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Response to Arguments
Applicant's arguments filed 02 February 2026 have been fully considered but the rejection is maintained in view of the arguments received 02 February 2026. However, upon further consideration, a new ground(s) of rejection is made in view of arguments received 13 January 2025.
The Applicant disagrees with the double patenting objection in the in the Office Action mailed 11 October 2024. The Applicant points to MPEP 608.01(m) for guidance. Regarding claims “3-5, 9, and 20”, “5, 7, and 16”, and “7, 9, and 19”, the Applicant states that the claims overlap subject matter and each claim is different in scope and breathe. The Applicant points to the MPEP 608.01(m) for guidance. The Applicant state “the invention in a reasonable number of ways. Indeed, a mere difference in scope between claims has been held to be enough.” [remarks, page 16].
In response, and as described above, the claims (i.e., grouped claims “3-5, 9, and 20”, “5, 7, and 16”, and “7, 9, and 19”) encompass the same limitations but grouped together. It is noted that although the claims were amended the claims were amended such that to not provide substantial duplicates. Here, as noted above, the claims remain substantial duplicates. Additionally, all the claims are dependent on claim 1. Thus, the claimed steps and limitations are substantial duplicates of each other and do not encompass different scopes and breathes. Therefore, the objection is maintained.
Conclusion
Claims 1-9, 11-13, and 15-20 are rejected.
No claims are allowed.
Finality
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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/J.C.P./ Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights