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 .
Applicants Amendment
Applicant’s amendment filed 1/21/2026 has been received and entered. Claim 1 has been amended, claims 2-9 have been deleted.
It is noted that claim 14 has also been amended, however the status identifier is indicated to be original.
Claims 1, 10-14 are pending.
Priority
This application filed 1/25/2022 claims benefit to US Provisional application 63/200612 filed 3/18/2021; and is related to PCT/US2022/13905 filed 1/26/2022.
Applicants have provided no comments regarding the summary of related applications.
Claim Objections
Claim 14 objected to because claim 14 has two periods at the end of the claim is withdrawn.
The amendment to the claim has addressed the basis of the rejection.
Appropriate correction is required.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
Response to Applicants arguments
Applicants acknowledge the rejections and indicate a terminal disclaimer would be filed when allowable subject matter is indicated in this or other applications.
In response, a rejection cannot be held in abeyance for prosecution of other applications. Since no specific arguments regarding obviousness or specific limitations have been made, the rejections have been updated and maintained.
The rejections have been updated to reflect the amendments to the claims.
Claims 1, 10-14 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-20 of copending Application No. 17/584073 (docketed, no action mailed). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of ‘073 are broader but have the same steps that encompass the evaluation of the interaction of two molecules which include small molecules interacting with a protein receptor (as provided in the specification, see page [0043] for the types of molecules and sources encompassed by the claims). The present claims provide for the necessary first steps in practicing ‘073 and assessing the chemical and physical structure and determining the fit of the two molecules. A copy of the pending independent method claim 1 of ‘073 is provided for comparison of the claims.
A method of generating at least one of the chemical and physical structure of at least one molecule having a property, comprising:
providing an initial molecule having at least one of a chemical structure and a physical structure;
selecting at least a first attribute of the initial molecule relating to a first property thereof; evaluating the performance of the first molecule with respect to the first property thereof; modifying at least a portion of the at least one of a chemical structure and a physical structure of the initial molecule to form a first modified molecule;
predicting the performance of the first modified molecule, upon further modification thereof, with respect to the performance of that first modified molecule with respect to the first property thereof; and
based on the predicted performance, further modifying the first modified molecule.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 10-14 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-20 of copending Application No. 17/584053 (docketed, no action mailed). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of ‘053 are broader but have the same steps that encompass the evaluation of the interaction of two molecules which include small molecules interacting with a protein receptor (as provided in the specification, see paragraphs [0003] and [0036] for the types of molecules and sources encompassed by the claims). The present claims provide for the necessary first steps in practicing ‘053 and assessing the chemical and physical structure and determining the fit of the two molecules. A copy of the pending independent method claim 1 of ‘053 is provided for comparison of the claims.
A method of designing molecules having one or more desired properties, comprising:
providing a plurality of known molecules having known properties as a first dataset; based on the properties of the known molecules, creating a plurality of new molecules having a structure different than that of at least one of the known molecules as a second data set;
evaluating the properties of the second dataset of molecules with respect to the desired properties to provide a score;
selecting a plurality of molecules from the second data set based on the score thereof to provide a nth scored dataset;
based on the properties of the second molecules, creating a plurality of new molecules in the nth data set;
selecting a plurality of molecules from the nth data set based on the score thereof to provide a nth + 1 scored dataset; and
repeating the acts of creating a plurality of new molecules based on the nth+1 data set to create the nth+2 data set; selecting a plurality of molecules from the nth +2 data set based on the score thereof to provide a nth + 3 scored dataset.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
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 reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim Rejections - 35 USC § 101
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, 10-14 stand rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim analysis
Claim 1 has been amended and still is generally directed to providing spatial data about two molecules and assessing the interaction of the two. More specifically, claim has been amended to incorporate the limitations of claims 2-9 (now cancelled). The claims limitations appear to have been addressed in the previous office action, where generally the claims are directed to steps which require ‘identifying’ spatial data for a candidate molecule and infectious agent and given the guidance of the specification this can be small molecules that interact with a protein associated with a virus or bacteria, and ‘determining’ if the molecule would bind the protein, and then assessing a pharmaceutical suitability broadly, but preferably as a form of potential treatment as a candidate molecule that affects the ‘infectious disease’ by reducing the infection or killing the virus/bacteria through the interaction of a candidate molecule and infectious agent in view of the guidance of the specification and in view of the art of record demonstrating research for anti-bacterial or anti-viral treatments.
Response to Applicants arguments
Applicants provide an overview of the intended use of the method outcome or analysis. Specifically, the use of transformer neural networks and providing the analysis in three dimensions to find agents to treat infection.
In response, the possible uses of suitable candidate molecules in acknowledged, however that is not part of the claim, nor a necessary outcome since it is a method of analysis and no specific data is required, simply methods of converting one form of data into another and generically ‘inputting the infectious agent start token to the numerical matrix representation of the infectious agent into a transformer neural network’. There are not specifics to how the TNN is created or how it works, just a generic indication to input data into it. The comparison to other types of neural networks is acknowledged and their difference, however this does not appear material to evaluating the claims. It is appreciated that different networks can function differently, however arguments that there is a complexity deficiency is not material because there is no required data or complexity set forth to the claims. The amendment to the claims appears to provide the limitations of dependent claims now cancelled, and there does not appear to be any specific argument or evidence of record that the combination of these limitations materially affect the computer environment or provide a practical application when the claim is viewed as a whole. Accordingly, for the reasons above and of record, the rejection is maintained.
As noted previously, one way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
The basis of the 101 analysis is updated and provided below for clarity of the record.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing spatial data of two things, a molecule and an agent. The step of determining if the two ‘would bind’ is an assessment of the spatial data, and based on that assessment the identification of ‘suitability’ are all considered to be part of the judicial exception. The judicial exception is a set of instructions to obtain data, assess it and provide a conclusion based on the assessment and appears to fall into the category of Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion). The claims do not require any specific spatial data noting that the data is not actively obtained but identified implying it exists, such as SMILES data from existing databases as suggested in the guidance of the specification. Further, claim 1 does not require any specific means of ‘determining’ and encompasses the visual assessment of two molecular models puzzled together. Dependent claims set forth for the use of a neural network generically and recite high level limitations that the data is presented as values in a matrix and an analysis that incorporates encoder and decoder blocks and the indication that multiple layers are configured for the analysis, however in the claims none of the steps are specifically set forth for the transformation of any and all forms of possible spatial data and subsequent analysis, where the analysis should assess the ability of the two to interact and ‘bind’. The final step for identification of suitability requires that the candidate molecule have a known property beyond the ability to bind, and in review of the specification no specific means for obtaining a property is provided for the vast number of possible candidate molecules and appears to be a requirement of some form of annotation on association which is known in the art and associated with the spatial data first obtained. The breadth of “identifying”, “determining”, and “a numerical matrix” in dependent claims encompasses non-transformative visual assessment of two structures. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using visual observation. Although the claims recite building and using a “matrix”, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Here, the independent claims do not require the use of a computer, and even as implied in the use of a ‘neural network’ the requirements of the claims only appear to broadly and generically indicate that any form of spatial data be somehow transformed into a numerical data which in turns is informative and can be used to assess the ability of two molecules to bind to each other. Further, the final step of a having a property implies pre-knowledge about the molecules being assessed and that the property somehow be associated as a possible therapeutic that is potentially associated with binding but more generally this is not required as how and what assessment is done to identify a ‘suitability’ of any potential candidate as a pharmaceutical is not present in the claims nor clearly defined in the specification. Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. The claims appear to fall into the category of concepts performed in the human mind which include observation, evaluation, judgment, opinion because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element. This judicial exception requires steps recited at high level of generality and to the extent it can be practiced using a computer are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining sequence data. As such, the claims do not provide for any additional element to consider under step 2B. It is noted in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence data. While the instruction are stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis.
The second part, Step 2B of the two step analysis is to determine whether any element or combination of elements, in the claim is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms (aligning sequences) to manipulate existing information (identify a probe that starts at a deletion or insertion) to generate additional information is not patent eligible. Furthermore, if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract idea (designing probes to a target sequence) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 10-14 are rejected under 35 U.S.C. 103 as being unpatentable over Ekins et al., Spagnoli et al. and Ebenezer et al.
Upon review, there is no specific teaching to use a transformer neural network. While the use of machine learning for structure analysis was performed given the evidence of record, the use of TNN was not.
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 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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