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 .
Status of the Claims
Claims 1-4 are pending and examined herein.
Claims 5-11 are withdrawn following an election made without traverse in the reply filed on 20 December 2023.
Claims 12-23 are canceled.
Priority
As detailed on the 24 April 2020 filing receipt, the application claims priority as early as 17 October 2017. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Claim Interpretation
In the specification, a "probe" is interpreted to refer to an amino acid, a "target structure" is interpreted to refer to a compound, and a "plurality of unit structures" is interpreted to refer to a plurality of atoms (pg. 3, paragraph [10]). In a broadest reasonable interpretation, these are interpreted as in silico representations of the molecules.
The term "feature quantity" is not defined. It occurs in the specification as "a descriptor (feature quantity)" (pg. 2, paragraph [5]), and a "fingerprint" is used as an example. Therefore, this term will be interpreted as any kind of quantitative feature of the molecule representation.
Claim Objections
The objections to claim 1 regarding the colon/semicolon and list elements are withdrawn.
The objection to claim 1 regarding reciting “designating compound” and should likely read “designating a compound” is maintained.
Claim 1 is further objected to because it recites “calculating... a spatial distribution... of free energy felt by each atom “μ” of an amino acid “a” (a represents a number representing a kind of amino acid; 1 to 20).” For clarity, this element should read “...of an amino acid “a”, [[(]]where a represents a number representing a kind of amino acid[[;]] 1 to 20[[)]]”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The rejections under 35 USC 112(b) are withdrawn in view of amendment regarding relative terms and different evaluation value calculating steps.
Claim Rejections - 35 USC § 112(a)
The rejection under 35 USC 112(a) is withdrawn in view of amendment removing calculating a degree of matching and adding comparison to a threshold as found in the written description.
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 1-4 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than the abstract idea of "feature quantity calculating."
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prone One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of
Matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is
the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method (claims 1-4), which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Claim 1 recites designating a compound as the target, where designating is interpreted as a data selection and thus performable by the human mind and is a mental process.
The claims recite calculating a first evaluation value reflecting intermolecular interaction properties contributing to binding the target protein by quantifying degree of accumulation of probes by the generated three dimensional structure, where calculations of values based on the structure is interpreted on a mental step of determining numerical values based on observe properties then a mathematical step of calculating a total evaluation value. Calculating the second evaluation value similarly rejected.
The claims recite calculating similarity between the first and second evaluation values. This step is interpreted as a comparison of numerical values and thus may be performed mentally, as the human mind is practically equipped to perform a comparison of two values, or as a mathematical concept such as determining a difference.
Claim 1 recites extracting compounds. The compounds are data in memory, and their extraction is interpreted as their selection. Data is abstract, and selection is a step the human mind is practically equipped to perform. Satisfying a threshold is interpreted as a data comparison set and thus practically performed by the human mind.
Claim 1 further recites "the distribution function… is obtained by geometrically averaging the distribution function… for each atom" and calculating the evaluation value in mathematical and verbal terms. A mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation (MPEP 2106.04(a)(2)).
Dependent claim 2 recites "quantifying… a degree of accumulation," where quantification is interpreted as arithmetic and therefore an abstract idea. Dependent claim 3 recites a step "converting the first feature into an invariant," which is interpreted as a mathematical concept. Dependent claim 4 recites a calculating step and therefore is interpreted as a mathematical concept.
Thus, the claims recite abstract ideas and thus must be examined further to determine whether elements in addition to the abstract ideas integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
Claim 1 recites “a computer,” “an external database,” “a network,” "one or more central processing units “storing, in a storage,” and "generating a three-dimensional structure."
The computer, database, processors, and network are interpreted as general purpose computer elements. The claims do not describe any specific computational steps by which the computer performs or carries out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than that a generic computer performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Claim 1 also recites "generating a three-dimensional structure" which is performed in preparation of the mathematical steps and is interpreted as insignificant extra solution activity (MPEP 2106.05(g)), which is required to perform the evaluation value calculation step.
The recited storing data in storage is for collecting information prior to an extracting step, and thus is interpreted as insignificant extra solution activity (MPEP 2106.05(g)).
The dependent claims do not recite any elements in addition to the abstract ideas. Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are directed to that abstract idea. Claims that are directed to abstract ideas must be examined further to determine whether the additional elements besides the abstract idea render the claims significantly more than the abstract idea. Claims that are directed to abstract ideas and that raise a concern of preemption of those abstract ideas must be examined to determine what elements, if any, they recite besides the abstract idea, and whether these additional elements constitute inventive concepts that are sufficient to render the claims significantly more than the abstract idea (MPEP 2106.05). [Step 2A Prong Two: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
Claim 1 recites “a computer,” “an external database,” “a network,” "one or more central processing units “storing, in a storage,” and "generating a three-dimensional structure." Claim 2 also recites data storage.
As explained above, the recited computer amounts to using a computer as a tool to perform an abstract idea (MPEP 2106.05(f)). The recited "storing" step, which is interpreted as requiring a computer, is further interpreted as storing and retrieving information in memory (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93) and therefore well-understood, routine, and conventional (MPEP 2106.05(d)(II)(iv)). The step of performing the data screening over a network is also interpreted as a conventional computer task (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014)).
Claim 1 additionally claims generating a three-dimensional structure formed by a plurality of units. Cozzini (Current Medicinal Chemistry 11: 3093-3118, 2004; previously cited on the 10 June 2025 PTO-892 form) teaches a review of computing free energy associated with macromolecules based on force fields (abstract) and the importance of obtaining a three-dimensional structure to determine binding to active sites (pg. 3093, col. 2, paragraph 1) and comparison to a reference in a database (pg. 3104, col. 1, last paragraph).
Therefore, none of the claims recite additional elements which would clearly amount to significantly more. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Response to the 20 August 2026 Applicant Remarks
Applicant remarks assert the screening using an external database is not intended use (pg. 10), which is persuasive.
Applicant remarks state the evaluation incorporates real physical constraints governing molecular binding and as such provide accurate identification from the database of likely binders with the desired properties, thus enhancing precision (pg. 10, third paragraph). Whether data is representative a real constraints does not affect the evaluation being based on data and not a collection of data from actual molecules. That is, the data collection is not an element in addition to the abstract ideas which would be evaluated at Steps 2A Prong Two and 2B of 101 analysis but rather as data per se, which is abstract.
Applicant remarks state the extracting step, which is based on comparison of a first evaluation value to a threshold value, which increases the speed of screening, thus improving computer technology (pg. 10, last paragraph). However, the improvement lies in the abstract idea of comparison of a numerical value to a threshold. The computer itself is not being improved. Using less data speeding up the processing is not a computer improvement but one directed to data analysis.
Thus, the rejection under 35 USC 101 is maintained.
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).
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.
Claims 1-4 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-2 and 7 of U.S. Patent No. US 12,542,197 B2 in view of the disclosure of the same. The reference disclosure teaches the importance of invariant descriptors as compounds having the same invariant structures have similar drug efficacies (pg. 11, paragraph [162]). The claims are both directed to the shared field of endeavor of feature quantity calculation and screening, and their combination would be expected to succeed. Therefore, the invention is prima facie obvious.
Reference claim 7 teaches the limitations of claim 1, including storing a first feature quantity, interpreted as similar to the first evaluation value, and making a similar calculation for a ligand which has a confirmed relationship to the target, calculating a similarity, and extracting similar compounds. Reference claim 2, parent to reference claim 7, recites designating a target and quantification calculating by degree of accumulation. Reference claim 1 recites designating a target, generating a three-dimensional structure, calculating a value – interpreted as a feature – based on the structure and binding affinity.
The reference claims do not teach the equations recited in the instant claims, which are found in the specification of the reference claims (paragraphs [144-145]).
Reference claim 2 teaches the limitations of instant claim 2 except that the structure is generated by a plurality of atoms in the generating step, which is disclosed by the reference specification (paragraph [22]).
Instant claim 3 is not taught by the reference claims but is disclosed by the reference specification (paragraph [19]).
Instant claim 3 is not taught by the reference claims but is disclosed by the reference specification (paragraph [155]).
Response to the 20 August 2026 Applicant Remarks
Applicant remarks state the rejection is traversed but requests the applicant be held in abeyance until the allowable subject matter is identified (pg. 11). As allowable subject matter has not been identified, the double patenting rejection is maintained.
Conclusion
THIS ACTION IS MADE FINAL. 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 Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia M. Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
