Prosecution Insights
Last updated: July 17, 2026
Application No. 18/065,271

COMPUTER-READABLE RECORDING MEDIUM STORING COMPOUND SUBSTITUTION PROGRAM, METHOD, AND DEVICE

Non-Final OA §101§102§112§DP
Filed
Dec 13, 2022
Priority
Jul 27, 2020 — continuation of PCTJP2020028718
Examiner
WISE, OLIVIA M.
Art Unit
Tech Center
Assignee
Fujitsu Limited
OA Round
1 (Non-Final)
34%
Grant Probability
At Risk
1-2
OA Rounds
4m
Est. Remaining
64%
With Interview

Examiner Intelligence

Grants only 34% of cases
34%
Career Allowance Rate
92 granted / 270 resolved
-25.9% vs TC avg
Strong +30% interview lift
Without
With
+30.0%
Interview Lift
resolved cases with interview
Typical timeline
3y 11m
Avg Prosecution
13 currently pending
Career history
322
Total Applications
across all art units

Statute-Specific Performance

§101
16.2%
-23.8% vs TC avg
§103
60.5%
+20.5% vs TC avg
§102
7.1%
-32.9% vs TC avg
§112
4.6%
-35.4% vs TC avg
Black line = Tech Center average estimate • Based on career data from 270 resolved cases

Office Action

§101 §102 §112 §DP
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 . Claim Status Claims 1-5 are currently pending and under exam herein. Claims 1-5 are rejected. Claims 1-3 are objected to. Priority The instant application also claims benefit to International Application PCT/JP2020/028718 filed on July 27, 2020. Domestic priority benefit is acknowledged. Thus, the effective filing date of Claims 1-5 is July 27, 2020. Information Disclosure Statement The information disclosure statement (IDS) was filed on 12/13/2022. All references in the IDS have been considered by the examiner and attached in this office action. Drawings The drawings filed on 12/13/2022 are accepted. Specification The Specification filed on 12/13/2022 is accepted. Claim Objections Claim 1 is objected to because of the following informalities: “to execute processing comprising:” should read “to execute processes comprised of:”. Claim 2 is objected to because of the following informalities: “the specifying processing includes processing of specifying candidates” should read “the specifying process includes specifying candidates”. Claim 3 is objected to because of the following informalities: “to execute processing comprising:” should read “to execute processes comprised of:” and “the generating processing is executed in a case where that the second compound is existable” should read “the generating process is executed when the second compound is existable”. Appropriate correction is required. Claim Rejections - 35 USC § 112 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. Claim 3 is 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. Claim 3 is dependent on claim 1, which recites “generating information that indicates a second compound…” as a required step within the process. However, claim 3, the dependent claim, recites that the generating process is only executed “in case where that the second compound is existable”. This claim limitation makes the originally required generating step of claim 1, a conditional step that is only carried out if the second compound is deemed existable. The claim is now considered indefinite because there is a question or doubt as to whether the generating process/step is necessary for the claim limitations, and thereby rendering the scope of the claim uncertain. The following is a quotation of 35 U.S.C. 112(d): (d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph: Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. Claim 3 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 3 is dependent on claim 1, which recites “generating information that indicates a second compound…” as an essential step within the process. However, claim 3, the dependent claim, recites that the generating process is only executed “in case where that the second compound is existable”. This claim limitation makes the originally required generating step of claim 1, a conditional step that is only carried out if the second compound is deemed existable, which further broadens the claim. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. 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 1-5 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea: Claim 1 recites specifying a first partial structure in a first compound (Abstract Idea: mental process) and referring to information that indicates relationships between a plurality of partial structures and selecting a second partial structure related to the first partial structure (Abstract Idea: mental process). Then the claim recites specifying a bond position in the second partial structure based on a rational formula (Abstract Idea: mental process), and finally generating information regarding a second compound obtained by substituting the first partial structure of the first compound with the second partial structure (Abstract Idea: mental process). The step of picking a partial structure from a compound is a simple process that can be merely drawing a circle over a substituent group in a chemical, which can be practically performed in the human mind or with pen and paper, making the limitation a mental process under the umbrella of abstract ideas. Similarly, analyzing other partial structures related to the first partial structure to pick a second partial structure can be as simple as picking another element (oxygen over hydrogen) replacement, which can also be practically performed in the human or with the aid of pen and paper, making the step of selecting a second partial structure a mental process as well. Next, determining the bonding position of the second partial structure based on known bonding rules and formulas is a process that can be done in the human mind as well, which again would make the claim limitation of specifying a bonding position a mental process. Finally, creating a second compound by substituting the first partial structure with the second partial structure based on known bonding information and generating information regarding the second compound is a process that can be practically carried out in the human mind with the assistance of pen and paper. Therefore, the step of creating the second compound based on partial structure substitution and generating information regarding the second compound would be a mental process, under abstract ideas. Claim 2 recites that the process of specifying a bonding position includes selecting candidates from a plurality of bonding positions based on types and valence of atoms included in the second partial structure (Abstract Idea: mental process). This is a process merely goes over known information regarding bonding information to select the optimal choice, which can be done practically in the human mind or with the assistance of a pen and paper, hence this limitation would constitute a mental process. Claim 3 recites confirming whether or not the second compound obtained by substituting the first partial structure with the second partial structure exists based on steric structures (Abstract Idea: mental process). Then, based on whether or not the second compound exists, the claim further generates information regarding the second compound (Abstract Idea: mental process). The act of confirming whether or not the second compound would exist based on known steric information is something that can be done in the human mind easily. In addition, generating information regarding a compound after deciding that it exists, may be as simple as generating a name for the compound, which is a process that can be practically done in the human mind. Hence both of these limitations would constitute a mental process under abstract ideas. Claim 4 recites a compound substitution method. The claim starts by specifying a first partial structure in a first compound (Abstract Idea: mental process) and referring to information that indicates relationships between a plurality of partial structures and selecting a second partial structure related to the first partial structure (Abstract Idea: mental process). Then the claim recites specifying a bond position in the second partial structure based on a rational formula (Abstract Idea: mental process), and finally generating information regarding a second compound obtained by substituting the first partial structure of the first compound with the second partial structure (Abstract Idea: mental process). The step of picking a partial structure from a compound is a simple process that can be merely drawing a circle over a substituent group in a chemical, which can be practically performed in the human mind or with pen and paper, making the limitation a mental process under the umbrella of abstract ideas. Similarly, analyzing other partial structures related to the first partial structure to pick a second partial structure can be as simple as picking another element (oxygen over hydrogen) replacement, which can also be practically performed in the human or with the aid of pen and paper, making the step of selecting a second partial structure a mental process as well. Next, determining the bonding position of the second partial structure based on known bonding rules and formulas is a process that can be done in the human mind as well, which again would make the claim limitation of specifying a bonding position a mental process. Finally, creating a second compound by substituting the first partial structure with the second partial structure based on known bonding information and generating information regarding the second compound is a process that can be practically carried out in the human mind with the assistance of pen and paper. Therefore, the step of creating the second compound based on partial structure substitution and generating information regarding the second compound would be a mental process, under abstract ideas. Claim 5 recites specifying a first partial structure in a first compound (Abstract Idea: mental process) and referring to information that indicates relationships between a plurality of partial structures and selecting a second partial structure related to the first partial structure (Abstract Idea: mental process). Then the claim recites specifying a bond position in the second partial structure based on a rational formula (Abstract Idea: mental process), and finally generating information regarding a second compound obtained by substituting the first partial structure of the first compound with the second partial structure (Abstract Idea: mental process). The step of picking a partial structure from a compound is a simple process that can be merely drawing a circle over a substituent group in a chemical, which can be practically performed in the human mind or with pen and paper, making the limitation a mental process under the umbrella of abstract ideas. Similarly, analyzing other partial structures related to the first partial structure to pick a second partial structure can be as simple as picking another element (oxygen over hydrogen) replacement, which can also be practically performed in the human or with the aid of pen and paper, making the step of selecting a second partial structure a mental process as well. Next, determining the bonding position of the second partial structure based on known bonding rules and formulas is a process that can be done in the human mind as well, which again would make the claim limitation of specifying a bonding position a mental process. Finally, creating a second compound by substituting the first partial structure with the second partial structure based on known bonding information and generating information regarding the second compound is a process that can be practically carried out in the human mind with the assistance of pen and paper. Therefore, the step of creating the second compound based on partial structure substitution and generating information regarding the second compound would be a mental process, under abstract ideas. These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” groupings of abstract ideas. While claims 1-3 and 5 recite performing some aspects of the analysis with a “program” or “device”, there are no additional limitations that indicate that this program or device requires anything other than carrying out the recited mental process in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claims 1-5 recite an abstract idea (Step 2A, Prong 1: YES). Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment. Specifically, the claims recite the following additional elements: Claim 1-3 recites a non-transitory computer-readable recording medium that stores a program. Claim 5 recites a device that has a memory and a processor coupled to the memory. There are no limitations that indicate that the claimed computer readable medium or device require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. In general, linking the use of an abstract idea to a particular technological environment, such as a computer, does not integrate the abstract idea into a practical application based on MPEP 2106.05(h). As such, claims 1-5 are directed to an abstract idea as the additional elements do not integrate the judicial exceptions into a practical application (Step 2A, Prong 2: NO). Claims found to be directed to a judicial exception under Step 2A, Prong 2 are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). In claims 1-5, there are no further limitations or additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic computing environment. According to MPEP 2106.05(d), courts have held computer‐implemented processes not to be significantly more than an abstract idea (and thus ineligible) where the claim as a whole amount to nothing more than generic computer functions merely used to implement an abstract idea, such as an idea that could be done by a human analog (i.e., by hand or by merely thinking). The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. As such, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). Therefore, claims 1-5 are not patent eligible. Claim Rejections - 35 USC § 102 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention. Claims 1-5 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ertl et al. (Journal of Computer-Aided Molecular Design Vol 26 pgs. 1207-1215, Published Sep 28, 2012). With respect to claim 1, Ertl et al. teaches a software system called IADE that generates automatic design of non-classical bioisosteric analogs through scaffold hopping, and fragment growing (pg. 1207 left col para 1, a non-transitory computer-readable recording medium storing a compound substitution program for causing a computer to execute processing). Ertl et al. states the program starts by fragmenting a template ligand into two fragments consisting of substituents (target fragment) and the rest of the molecule (pg. 1208 right col para 2 and pg. 1209 Fig. 2, specifying a first partial structure included in a first compound). Next, Ertl et al. states that bioisosteric fragments (chemical substituents that share similar physical or chemical properties) are then identified from a database of more than 10,000 common substituents based on their similarity to the target fragment (pg. 1208 right col para 3 and pg. 1210 Fig. 3, referring to information that indicates a relationship between a plurality of partial structures and selecting a second partial structure related to the first partial structure). Ertl et al. takes it one step further and also looks at descriptors characterizing bond connections for these bioisosteric fragments such as electron donating or accepting power at connection points, size of the fragments base on atom counts, and fragment shape in order to determine the best link between the fragment and the rest of the molecule (pg. 1209 left col para 1, specifying a bonding position in the second partial structure based on a rational formula of the selected second partial structure). Then, Ertl et al. generates new analog molecules based on the replacement of the target fragment with the identified bioisosteric fragment (pg. 1209 left col para 2 – right col para 1). Finally, Ertl et al. takes the analog molecules and converts them into 3D models through CORINA in order to generate representative conformation information based on positive, negative, hydrophobic and steric fields around the molecule (pg. 1209 right col para 2- pg. 1210 left col para 1, generating information that indicates a second compound obtained by substituting the first partial structure of the first compound with the second partial structure, based on the specified bonding position). Regarding claim 2, Ertl et al. discloses the use of descriptors characterizing bond connections for the bioisosteric fragments such as electron donating or accepting power at connection points, size of the fragments base on atom counts, and fragment shape in order to determine the best link between the fragment and the rest of the molecule (pg. 1209 left col para 1, the specifying processing includes processing of specifying candidates of a plurality of bonding positions, based on types and valence of atoms included in selected second partial structure). Concerning claim 3, Ertl et al. teaches the conversion of the generated new analog molecules into 3D models with CORINA in order to determine that the structure is indeed existable in 3D space based on superposition of positive, negative, hydrophobic and steric fields around the molecules and then generating the representative conformation information (pg. 1209 right col para 2- pg. 1210 left col para 1, confirming whether or not a second compound obtained by substituting the first partial structure of the first compound with the second partial structure based on the specified bonding position is existable as a steric structure, wherein the generating processing is executed in a case where that the second compound is existable as the steric structure is confirmed). With respect to claim 4, Ertl et al. teaches a software system called IADE that generates automatic design of non-classical bioisosteric analogs through scaffold hopping, and fragment growing (pg. 1207 left col para 1, a compound substitution method). Ertl et al. states the program starts by fragmenting a template ligand into two fragments consisting of substituents (target fragment) and the rest of the molecule (pg. 1208 right col para 2 and pg. 1209 Fig. 2, specifying a first partial structure included in a first compound). Next, Ertl et al. states that bioisosteric fragments (chemical substituents that share similar physical or chemical properties) are then identified from a database of more than 10,000 common substituents based on their similarity to the target fragment (pg. 1208 right col para 3 and pg. 1210 Fig. 3, referring to information that indicates a relationship between a plurality of partial structures and selecting a second partial structure related to the first partial structure). Ertl et al. takes it one step further and also looks at descriptors characterizing bond connections for these bioisosteric fragments such as electron donating or accepting power at connection points, size of the fragments base on atom counts, and fragment shape in order to determine the best link between the fragment and the rest of the molecule (pg. 1209 left col para 1, specifying a bonding position in the second partial structure based on a rational formula of the selected second partial structure). Then, Ertl et al. generates new analog molecules based on the replacement of the target fragment with the identified bioisosteric fragment (pg. 1209 left col para 2 – right col para 1). Finally, Ertl et al. takes the analog molecules and converts them into 3D models through CORINA in order to generate representative conformation information based on positive, negative, hydrophobic and steric fields around the molecule (pg. 1209 right col para 2- pg. 1210 left col para 1, generating information that indicates a second compound obtained by substituting the first partial structure of the first compound with the second partial structure, based on the specified bonding position). Regarding claim 5, Ertl et al. teaches a software system called IADE, which is inherently carried out on a computer with memory and a processor, that generates automatic design of non-classical bioisosteric analogs through scaffold hopping, and fragment growing (pg. 1207 left col para 1, a device comprising: a memory; and a processor coupled to the memory and configured to). Ertl et al. states the program starts by fragmenting a template ligand into two fragments consisting of substituents (target fragment) and the rest of the molecule (pg. 1208 right col para 2 and pg. 1209 Fig. 2, specifying a first partial structure included in a first compound). Next, Ertl et al. states that bioisosteric fragments (chemical substituents that share similar physical or chemical properties) are then identified from a database of more than 10,000 common substituents based on their similarity to the target fragment (pg. 1208 right col para 3 and pg. 1210 Fig. 3, referring to information that indicates a relationship between a plurality of partial structures and selecting a second partial structure related to the first partial structure). Ertl et al. takes it one step further and also looks at descriptors characterizing bond connections for these bioisosteric fragments such as electron donating or accepting power at connection points, size of the fragments base on atom counts, and fragment shape in order to determine the best link between the fragment and the rest of the molecule (pg. 1209 left col para 1, specifying a bonding position in the second partial structure based on a rational formula of the selected second partial structure). Then, Ertl et al. generates new analog molecules based on the replacement of the target fragment with the identified bioisosteric fragment (pg. 1209 left col para 2 – right col para 1). Finally, Ertl et al. takes the analog molecules and converts them into 3D models through CORINA in order to generate representative conformation information based on positive, negative, hydrophobic and steric fields around the molecule (pg. 1209 right col para 2- pg. 1210 left col para 1, generating information that indicates a second compound obtained by substituting the first partial structure of the first compound with the second partial structure, based on the specified bonding position). 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 1-5 are provisionally rejected on the ground of non-statutory double patenting as being unpatentable over claims 1, 5-7 of co-pending Application No. 18/065,443. Although the claims at issue are not identical, they are not patentably distinct from each other. This is a provisional non-statutory double patenting rejection. Claims 1-3 recites a non-transitory computer-readable recording medium storing a compound substitution program that specifies a first partial structure in a first compound, and a second partial structure related to the first partial structure based on information indicating a relationship between the two partial structures. Claims 1-2 then teaches obtaining a second compound by substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. Claim 3 on the other hand teaches only generating information regarding the second compound if it is deemed existable. In patent Application No. 18/065,443, claim 1 also claims a non-transitory computer-readable recording medium storing a compound substitution program that specifies a first partial structure in a first compound, and a second partial structured related to the first partial structure based on information indicating a relationship between the two partial structures. Claim 1 of Application No. 18/065,443 then goes on to generate a second compound by also substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. Similar to claim 3 of the instant application, claim 5 of Application No. 18/065,443 also only generates information regarding the second compound only if a score is above a certain threshold. However, the instant application further adds to the program by specifying bond positions in the second partial structure based on type and valences of atoms in the second partial structure with a rational formula (claim 1 and 2) which was not explicitly recited in the claim limitations of the reference application. Yet this claim limitation is an obvious step in the compound substitution program as once a second partial structure is selected it would have been an obvious matter of routine optimization to one of ordinary skill in the art to determine the way that the second partial structure would need to bond to the first compound in order to generate a chemically valid substituted compound. Claim 4 recites a compound substitution method that specifies a first partial structure in a first compound, and a second partial structure related to the first partial structure based on information indicating a relationship between the two partial structures. Claim 4 then teaches obtaining a second compound by substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. In patent Application No. 18/065,443, claim 6 also claims a compound substitution method that specifies a first partial structure in a first compound, and a second partial structured related to the first partial structure based on information indicating a relationship between the two partial structures. Claim 6 of Application No. 18/065,443 then goes on to generate a second compound by also substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. However, claim 4 of the instant application further adds to the program by specifying a bond position in the second partial structure based on rational formula, which was not explicitly recited in the claim limitations of the reference application. Yet this claim limitation is an obvious step in the compound substitution program as once a second partial structure is selected it would have been an obvious matter of routine optimization to one of ordinary skill in the art to determine the way that the second partial structure would need to bond to the first compound in order to generate a chemically valid substituted compound. Claim 5 recites a device with memory and a processor configured to specify a first partial structure in a first compound, and a second partial structure related to the first partial structure based on information indicating a relationship between the two partial structures. Claim 5 then teaches obtaining a second compound by substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. In patent Application No. 18/065,443, claim 7 also claims device with a memory and a processor coupled to the memory and configured to specify a first partial structure in a first compound, and a second partial structured related to the first partial structure based on information indicating a relationship between the two partial structures. Claim 7 of Application No. 18/065,443 then goes on to generate a second compound by also substituting the first partial structure in the first compound with the second partial structure and generating information on the second compound. However, claim 5 of the instant application further adds to the program by specifying a bond position in the second partial structure based on rational formula, which was not explicitly recited in the claim limitations of the reference application. Yet this claim limitation is an obvious step in the compound substitution program as once a second partial structure is selected it would have been an obvious matter of routine optimization to one of ordinary skill in the art to determine the way that the second partial structure would need to bond to the first compound in order to generate a chemically valid substituted compound. Both applications share substantially identical core inventive concepts, specifically, selecting a related second partial structure using relation information to a first partial structure in order to generate a second compound through partial structure substitution. Accordingly, the instant claims are not patentably distinct from the claims of Application No. 18/065,443. Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to WENYU YANG whose telephone number is (571)272-0035. The examiner can normally be reached 8:30am - 5:00 pm. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia 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. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /W.Y./Examiner, Art Unit 1685 /OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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Prosecution Timeline

Dec 13, 2022
Application Filed
Jun 10, 2026
Non-Final Rejection mailed — §101, §102, §112 (current)

Precedent Cases

Applications granted by this same examiner with similar technology

Patent 11984195
METHYLATION PATTERN ANALYSIS OF TISSUES IN A DNA MIXTURE
5y 7m to grant Granted May 14, 2024
Patent 11965892
HLA-BASED METHODS AND COMPOSITIONS AND USES THEREOF
4y 8m to grant Granted Apr 23, 2024
Patent 11954614
SYSTEMS AND METHODS FOR VISUALIZING A PATTERN IN A DATASET
4y 9m to grant Granted Apr 09, 2024
Patent 11858994
NOVEL BIOMARKERS FOR CANCER IMMUNOTHERAPY
4y 3m to grant Granted Jan 02, 2024
Patent 11851710
METHODS AND MATERIALS FOR IDENTIFYING METASTATIC MALIGNANT SKIN LESIONS AND TREATING SKIN CANCER
4y 3m to grant Granted Dec 26, 2023
Study what changed to get past this examiner. Based on 5 most recent grants.

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Prosecution Projections

1-2
Expected OA Rounds
34%
Grant Probability
64%
With Interview (+30.0%)
3y 11m (~4m remaining)
Median Time to Grant
Low
PTA Risk
Based on 270 resolved cases by this examiner. Grant probability derived from career allowance rate.

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