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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 7/15/2025 has been entered.
Status of Claims
Claims 2, 5, 15 and 17-20 are cancelled.
Claims 1, 3-4, 6-14, 16, 21-25 are pending and are examined on the merits.
Priority
As detailed on the 09/02/2022 filing receipt, this application claims benefit over a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c). Priority of US application 62/359,663 filed 07/07/2016 is acknowledged.
Claim Rejections - 35 USC § 101
The instant rejection is maintained from the previous Office Action filed 4/15/2025 and modified in view of Applicant’s amendments filed 7/15/2025.
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, 3-4, 6-14, 16, 21-25 are rejected under 35 USC 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1, 3-4, 6-14, 16, 21-25 are directed to a 101 process, here a "method," for generating a set of chemical candidates predicted to interact with a binding target.
Step 2A Prong One: Identification of an Abstract Idea
Claim 1 recites:
1. Generating, using a computational model, a set of chemical candidates, the computational model trained to receive, as input, a binding target and provide, as output, one or more chemical candidates predicted to interact with the binding target.
This step recites the operation of a trained computational model. Except the input and output, no specific parameters are provided about the model. Under a Broadest Reasonable Interpretation (BRI), the operation of the model is interpreted as mathematical calculations. The step hence equates to the abstract idea of mathematical concepts. The step can also be performed by the human mind by comparing a binding target to a list of chemical candidate that would interact with the binding target to generate (i.e. select) chemical candidates.
2. Establishing a plurality of chemical pairs, each chemical pair including the chemical candidate and a respective one of a plurality of chemical controls, each of the plurality of chemical controls known to bind with the binding target.
This step recites data manipulation (establishing a plurality of pairs from candidates and controls). The step hence equates to the abstract idea of mental activities.
3. Comparing, for each pair of the plurality of chemical pairs, values of at least two datatypes comprising a first datatype and a second datatype of the chemical candidate to values of the first datatype and the second datatype of the respective one of the plurality of chemical controls in the pair to generate a first similarity score for the first datatype a second similarity score for the second datatype;
This step recites data observation (“comparing”) and mathematical operations (“to generate a similarity score”). The step hence equates to the abstract idea of mental activities and mathematical concepts.
4. Converting, the first similarity score to a first likelihood value and a second similarity score to a second likelihood value, the first likelihood value and the second likelihood value indicating likelihoods that the chemical candidate and the respective one of the plurality of chemical controls include in the corresponding chemical pair have a shared binding target based on the respective one of the first datatype and the second datatype.
This step equates to data manipulation through mathematical operations, which is an abstract idea of mathematical concepts.5. Determining, for each chemical pair, a total likelihood value based on the first and second likelihood values;
This step recites mathematical operations (determining … a total likelihood value…”). This step equates to abstract idea of mathematical concepts.
6. Identifying that the chemical candidate is predicted to bind to the binding target based on the total likelihood values of the plurality of pairs.
This step equates to a decision-making based on data observation, which is an abstract idea of mental activities.
7. Ranking, based on the total likelihood values, chemical candidates in the set of chemical candidates to obtain a ranked set of chemical candidates;
This step recites ranking by the total likelihood values, which reads on a mental activity of judgement that can be accomplished in human mind. Hence this step equates to an abstract idea of mental processes.
Therefore, these limitations fall under the “mental process” and “mathematical concepts” groupings of abstract ideas. Dependent claims 3-4, 6-14, 16, 21-25 further recite additional limitations characterizing the computer model for predicting interaction pairs that read on mathematics or mental steps. The dependent claims are therefore drawn to further abstract idea steps.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a step of ranking chemical candidates based on likelihood values and then performing an experimental validation (“performing one or more assays to confirm that at least one of the chemical candidates physically interacts with the binding target”) of ranked prediction of chemical candidates. The claims do not recite additional elements that integrate the abstract idea into a practical application. Instead, the claims as a whole, reads on “apply it” based on the abstract ideas. Here the resulting step of ranking is not integrated into a practical application, i.e. so as to effect a transformation or reduction of a particular article to a different state or thing.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The following additional elements are recited in claims:
Performing one or more assays to confirm that at least one of the chemical candidates physically interacts with the binding target, each assay being either (i) an in-vitro assay using a preparation of the binding target or (ii) an ex-vivo assay carried out in a biological sample that contains the binding target, wherein at least one of the assays comprises:(a) measuring a change in biochemical activity of the binding target caused by the presence of the chemical candidate; or (b) detecting, by microscopy, a structural or organizational change in the binding target caused by the presence of the chemical candidate; and
providing the at least one physically-validated chemical candidate for development of a product for the binding target.
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, because these steps are routine, conventional and well understood in clinical development. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
As such, claims 1, 3-4, 6-14, 16, 21-25 are not patent eligible.
Response to Arguments
In the Remarks (pages 7-8) filed 15 July 2025, Applicant argues that the newly added additional elements in claim 1 integrate the alleged judicial exceptions into a practical application (page 7, last para through page 8, 3rd para). Applicant’s argument refers to Step 2A/Prong Two in the 101 analysis, relating to whether claims are integrated into a practical application due to technical improvements or not. The argument is not persuasive. Followed are the argued elements:
Performing one or more assays to confirm that at least one of the chemical candidates physically interacts with the binding target, each assay being either (i) an in-vitro assay using a preparation of the binding target or (ii) an ex-vivo assay carried out in a biological sample that contains the binding target, wherein at least one of the assays comprises:(a) measuring a change in biochemical activity of the binding target caused by the presence of the chemical candidate; or (b) detecting, by microscopy, a structural or organizational change in the binding target caused by the presence of the chemical candidate; and providing the at least one physically-validated chemical candidate for development of a product for the binding target. This additional element of assaying compounds does not guarantee a transformation of matter (which is one of the categories of practical application). Mixing or moving objects around is not deemed to be a practical application because it does not necessitate a particular transformation or reduction of a particular article to a different state or thing, as described in MPEP 2106.05(c). Without using the chemical binding reaction in a real-world situation, the recited abstract idea will not be integrated into a practical application. Categories of practical application are listed above under Step 2A Prong Two.
Therefore 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.
Hence, the 101 rejection is maintained.
Conclusion
No claims are allowed.
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/Anna Skibinsky/
Primary Examiner, AU 1635
/GL/
Patent Examiner
Art Unit 1686