Prosecution Insights
Last updated: July 17, 2026
Application No. 17/822,899

SYSTEM AND METHOD FOR DISCOVERING DRUG ACTIVE SITE OF PROTEIN USING PATHOGENIC MUTATION

Non-Final OA §103§112§DP
Filed
Aug 29, 2022
Priority
Aug 30, 2021 — RE 10-2021-0114968
Examiner
ELKINS, BLAKE HARRISON
Art Unit
1687
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
3Billion
OA Round
1 (Non-Final)
100%
Grant Probability
Favorable
1-2
OA Rounds
3m
Est. Remaining
99%
With Interview

Examiner Intelligence

Grants 100% — above average
100%
Career Allowance Rate
1 granted / 1 resolved
+40.0% vs TC avg
Minimal +0% lift
Without
With
+0.0%
Interview Lift
resolved cases with interview
Typical timeline
4y 1m
Avg Prosecution
16 currently pending
Career history
19
Total Applications
across all art units

Statute-Specific Performance

§103
8.8%
-31.2% vs TC avg
Black line = Tech Center average estimate • Based on career data from 1 resolved cases

Office Action

§103 §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 1-10 are currently pending and under examination herein. Claims 1-10 are rejected. Priority The application claims foreign priority to KR10-2021-0114968 filed 30 August 2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. In this action, claims 1-10 are examined as though they had an effective filing date of 30 August 2021. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s). Information Disclosure Statement The information disclosure statement(s) (IDS) submitted on 29 August 2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. Drawings The drawings filed 29 August 2022 are accepted. Specification The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Two web links were found in the specification (Page 12, Paragraph 0045). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http://, www., or other browser-executable code. See MPEP § 608.01. Claim Interpretation The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked. As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph: (A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function; (B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and (C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function. Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function. Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function. Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitations are: “a pathogenic mutation position detection unit for detecting a pathogenic mutation position” in claim 1. “a drug active site detection unit detecting a drug active site” in claim 1. Because these claim limitations are being interpreted under 35 U.S.C. 112(f), they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. However, no structure was found in the disclosure (See 112(a) and 112(b) rejections). If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Claim Rejections - 35 USC § 112 The following is a quotation of the first paragraph of 35 U.S.C. 112(a): (a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention. Claims 1-5 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. Claim 1 recites “a pathogenic mutation position detection unit” and “a drug active site detection unit detecting a drug” but provides no structure for the recited units within the disclosure (see Claim Interpretation – 112(f)). Claims 2-5 depend on Claim 1, and thus contain the above issues due to said dependence. 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. Claim 1-5 and 8-10 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. The claim 1 limitations “a pathogenic mutation position detection unit” and “a drug active site detection unit” invokes 35 U.S.C. 112(f). However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The disclosure is devoid of any structure that performs the function in the claim, such as a computer. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b). Claims 2-5 depend on Claim 1, and thus contain the above issues due to said dependence. For the purposes of examination, the units are interpreted as generic computing devices, such as a computer. Applicant may: (a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph; (b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)). If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either: (a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181. Claims 3 and 8 recite “a three-dimensional structure”. Claims 3 and 8 depend on 1 and 6 respectively, which recite “a three-dimensional structure”. It is unclear if these are the same are different three dimensional structures. The metes and bounds of these limitations are unclear rendering the claims indefinite. Claims 4-5 and 9-10 depend on Claims 3 and 8, and thus contain the above issue due to said dependence. This rejection can be overcome by amending claims 3 and 8 to “the three dimensional structure” if the structures are the same or creating a different name if there are multiple and different three dimensional structures being recited. Claim Rejections - 35 USC § 103 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. The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness. Claims 1-3, 5-8, and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Gao et al. (2015, Structure, Vol. 23: 1362–1369), in view of Jiang et al. (2019, BMC Bioinformatics, Vol. 20: 1-13). Italicized text from reference art. The applicable claims include: Claim 1. A system for discovering a drug active site of protein using a pathogenic mutation comprising: i. a pathogenic mutation position detection unit for detecting a pathogenic mutation position corresponding to a pathogenic mutation in a three-dimensional structure of protein, using pathogenic mutation data containing information on a pathogenic mutation causing an abnormal protein function and protein structure data containing information on the three-dimensional structure corresponding to genetic sequencing of the protein; and ii. a drug active site detection unit detecting a drug active site, corresponding to the pathogenic mutation position, and, to which a drug is bindable. Claim 2. The system according to claim 1, wherein the drug active site includes at least one among a structure directly exposed externally of the three-dimensional structure of the protein, and a structure exposed externally through a path connected externally of the three-dimensional structure. Claim 3. The system according to claim 1, wherein the drug active site detection unit detects an empty space, which i. is adjacent to the pathogenic mutation position in a protein model formed in a three-dimensional structure corresponding to each atom contained in the three-dimensional structure of the protein, ii. has a volume greater than or equal to a predetermined volume corresponding to the drug, and iii. is connected externally of the protein model, as the drug active site. Claim 5. The system according to claim 3, wherein a first coordinate included in the empty space is connected to a second coordinate located outside the protein model through a path spaced apart from the protein model. Claim 6. A method for discovering a drug active site of protein using a pathogenic mutation comprising: i. a pathogenic mutation position detecting operation of detecting a pathogenic mutation position corresponding to a pathogenic mutation in a three-dimensional structure of protein, using pathogenic mutation data containing information on a pathogenic mutation causing an abnormal protein function and protein structure data containing information on the three-dimensional structure corresponding to genetic sequencing of the protein; and ii. a drug active site detecting operation of detecting a drug active site, corresponding to the pathogenic mutation position, and, to which a drug is bindable. Claim 7. The method according to claim 6, wherein the drug active site includes at least one among a structure directly exposed externally of the three-dimensional structure of the protein, and a structure exposed externally through a path connected externally of the three-dimensional structure. Claim 8. The method according to claim 6, wherein the drug active site detecting operation is to detect an empty space, which i. is adjacent to the pathogenic mutation position in a protein model formed in a three-dimensional structure corresponding to each atom contained in the three-dimensional structure of the protein, ii. has a volume greater than or equal to a predetermined volume corresponding to the drug, and iii. is connected externally of the protein model, as the drug active site. Claim 10. The method according to claim 8, wherein a first coordinate included in the empty space is connected to a second coordinate located outside the protein model through a path spaced apart from the protein model. Regarding Claims 1 and 6, Gao et al. teach (Claim 1.i) pathogenic mutation position detection of detecting a pathogenic mutation position corresponding a three-dimensional structure of protein (Page 1363, Column 1, Paragraph 3: We have collected 6,025 disease-associated missense mutations in 642 human genes. All these mutations have at least one experimentally determined protein structure containing the corresponding mutation. The locations of these mutations are subsequently analyzed), using pathogenic mutation data on a pathogenic mutation causing an abnormal protein function and protein structure data containing information on the three-dimensional structure corresponding to genetic sequencing (Page 1363, Column 2, Paragraph 2: After these classifications, 17% of mutations are found in pockets, which might engage in unknown interactions with some biomolecules. Overall, this classification scheme could assign a primary functional or structural role for 70% of disease-associated mutations). Additionally, Gao et al. teach the recited methods are performed by a system (a computer), which would also include the pathogenic mutation position detection unit and drug active site detection unit (Page 1368, Column 2, Paragraph 1: Atomic contacts between protein and ligand were determined by the program LPC. Solvent accessible surface area (SASA) was calculated for each original residue of the mutations using the program NACCESS. Calculations of the free energy differences, DDG, of Trp mutations were conducted using the program DMutant). Claim 6 recites the limitations of claim 1 directed to a method. Regarding Claims 2 and 7, Gao et al. teach the drug active site includes a structure directly exposed externally of the three-dimensional structure of the protein, and a structure exposed externally through a path connected externally of the three-dimensional structure (Page 1363, Column 2, Paragraph 2: Figure 1 shows a pie chart obtained by assigning a unique primary location to each mutation, using the following order: DNA/ RNA binding, ion binding, small-molecule ligand binding, PPI, buried, EFICAz, FINDSITEcomb, pocket, and other exposed; Page 1367, Column 2, Paragraph 2: Mutations (i.e. sections associated with structures or binding sites) within interfacial pockets could disrupt functionally important ligand-protein interactions; Page 1368, Column 2, Paragraph 1 Otherwise, the residue is an exposed surface residue). In the art, mutation sites (i.e. a structure that could function as potential drug target site) are associated with pockets (i.e. cavities) which indicate the structure is exposed though a path connected externally. Claim 7 recites the limitations of claim 2 directed to a method. Regarding Claim 3 and 8, Gao et al. teach (Claim 3.ii) the drug active site detection detects an empty space which has a volume greater than or equal to a predetermined volume corresponding to the drug (Page 1363, Column 2, Paragraph 2: The remaining 30% of mutations involve exposed surface residues and are located at either a flat surface or small pocket. They are potentially candidate interaction sites for unknown protein-protein interactions or interactions with biomolecules that do not require large concave pockets). The sites selected correspond to locations that a biomolecule (i.e. the drug) is small enough to fit into (a small pocket) as they could not fit into a large pocket. Claim 8 recites the limitations of claim 3 directed to a method. Gao et al. does not teach drug active site detection detects a drug active site, corresponding to the pathogenic mutation position, and, to which a drug is bindable (Claims 1.ii and 6.ii). Gao et al. also does not teach the drug active site detection detects an empty space which is adjacent to the pathogenic mutation position in a protein model formed in a three-dimensional structure corresponding to each atom contained in the three-dimensional structure of the protein (Claims 3.i and 8.i). Gao et al. also does not teach the drug active site detection detects an empty space which is connected externally of the protein model, as the drug active site (Claims 3.iii and 8.iii). Gao et al. also does not teach a first coordinate included in the empty space is connected to a second coordinate located outside the protein model through a path spaced apart from the protein model (Claims 5 and 10). Regarding Claims 1 and 6, Jiang et al. teach (Claim 1.ii) a drug active site detection detects a drug active site, corresponding to the pathogenic mutation position to which a drug is bindable (Page 8, Column 2, Paragraph 2: we combined these two methods to construct a protein descriptor, which is adapted to deep learning specifically for the detection of the protein drug binding sites. The three-dimensional structure of the protein and the non-bonded interactions that influence the formation of the binding sites are introduced to construct the descriptor). As described above Jiang et al. uses the three dimensional structure, especially pockets, to identify the drug active site. However, this is not taught in the context of mutations. It would be obvious to utilize the mutations associated structures such as pockets taught by the methods of Gao et al. (see reason to combine). Claim 6 recites the limitations of claim 1 directed to a method. Regarding Claims 2 and 7, Jiang et al. teach the drug active site includes a structure directly exposed externally of the three-dimensional structure of the protein, and a structure exposed externally through a path connected externally of the three-dimensional structure (Page 12, Column 1, Paragraph 2: The output of the model is the probability that a sample block belongs to the binding site. At the same time, each pocket is scored based on the average predicted block probability values of each pocket). A pocket (i.e. cavity accessible to the exterior) as shown by Figure 8 (Page 9, Column 2) seems to be commensurate in scope with both a structure directly exposed externally and a structure exposed externally through a path connected externally. Claim 7 recites the limitations of claim 2 directed to a method. Regarding Claim 3 and 8, Jiang et al. teach (Claim 3.i) the drug active site detection detects an empty space which is adjacent to the pathogenic mutation position in a protein model formed in a three-dimensional structure corresponding to each atom contained in the three-dimensional structure (Page 8, Column 2, Paragraph 2: It is obvious that the geometry-based approaches take protein shape into consideration and look for gaps or cavities on the surface of a protein; Page 9, Column 2, Figure 8: The voxels represent the solvent (i.e. empty space), the green dots are the protein atoms, and the white area is the protein contour.) The binding site is identified based on an accessible pocket of empty space (see Regarding Claims 2 and 7). The identification is based on the structure and does not explicitly mention a mutation. It would be obvious to combine the binding site based structure identification method of Jiang et al. with the mutation plus structure identification method of Gao et al. (See Regarding Claims 1 and 6; also see reason to combine). Jiang et al. also teach (Claim 3.iii) the drug active site detection detects an empty space which is connected externally of the protein model, as the drug active site (Page 9, Column 1, Paragraph 2: Initially, a bounding box of a protein is constructed and an 8Å buffer is added to the surroundings of the box). Figure 8 (Page 9, Column 2) shows the empty space of the pockets connected the exterior of the protein (i.e. the buffer added to the bounding box of the protein). Claim 8 recites the limitations of claim 3 directed to a method. Regarding Claims 5 and 10, Jiang et al. teach a first coordinate included in the empty space is connected to a second coordinate located outside the protein model through a path spaced apart from the protein model (Page 9, Column 1, Paragraph 2: Initially, a bounding box of a protein is constructed and an 8Å buffer is added to the surroundings of the box; Page 9, Column 1, Paragraph 3: Then, the grid is scanned in x, y, z axes and four cubic diagonal directions). The grid system employed is used to detect pockets (i.e., empty space, see Regarding Claims 3 and 8) and utilizes coordinates (x, y, z positions) to track the voxels. Figure 8 (Page 9, Column 2) shows the empty space (i.e. pocket) connected, via the grid and coordinate system, to space outside the protein (i.e. the buffer). Claim 10 recites the limitations of claim 5 directed to a method. It would have been obvious to one of ordinary skill in the art at the time of the effective filing date to combine Gao et al. with Jiang et al. because Gao et al. teach their methods of mutation identification associated with structures are suitable for incorporating into binding site identification (Page 1363, Column 2, Paragraph 2: They are potentially candidate interaction sites for unknown protein-protein interactions or interactions with biomolecules that do not require large concave pockets; Page 1365, Column 2, Paragraph 2: One important benefit of an interfacial pocket formed adjacent to PPIs is that it could function as a molecular switch controlled by the association/ dissociation of the protein complex). The cited sections also make it obvious to implement these methods for binding cites related to drugs given the association to disease (Page 1365, Column 2, Paragraph 3: We examined how many disease-associated mutations are located at such a site compared with neutral mutations). Binding site identification, especially as it relates to drugs, is the primary goal of the highly effective methods proposed by Jiang et al. (Page 3, Column 1, Paragraph 3: In this work, a multi-channel molecular descriptor for the prediction of protein drug binding sites is proposed. The descriptor is more accurate than other methods of site prediction). Therefore, it would have been obvious to someone of ordinary skill in the art at the time of the effective filing date to combine the methods from the references indicated above. Furthermore, one of ordinary skill in the art would predict that the methods taught by Gao et al. could be readily combined with the method of Jiang et al. with a reasonable expectation of success because both are within the same technical field - modeling and making predictions based on three dimensional protein structure related to binding sites. Accordingly, 1-3, 5-8, and 10 taken as a whole would have been prima facie obvious before the effective filing date and are rejected under 35 U.S.C. 103. Claims 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over Gao et al., as applied to Claims 1-3, 5-8, and 10 above, in view of Jiang et al., as applied to Claims 1-3, 5-8, and 10 above, and in further view of Tubert-Brohman et al. (2013, Journal or Chemical Information and Modeling, Vol. 53: 1689−1699). Italicized text from reference art. The applicable claims include: Claims 1-3, 5-8, and 10 are listed above Claim 4. The system according to claim 3, wherein the three-dimensional structure has a radius at a predetermined ratio of Van der Waals Radius of each atom. Claim 9. The method according to claim 8, wherein the three-dimensional structure has a radius at a predetermined ratio of Van der Waals Radius of each atom. Regarding Claims 1-3, 5-8, and 10, these limitations are taught by Gao et al. and Jiang et al. as indicated above in the 103 rejection. Gao et al. and Jiang et al. do not teach the three-dimensional structure has a radius at a predetermined ratio of Van der Waals Radius of each atom (Claims 4 and 9). Regarding Claims 4 and 9, Tubert-Brohman et al. teach the three-dimensional structure has a radius at a predetermined ratio of Van der Waals Radius of each atom (Page 1697, Column 1, Paragraph 2: We implemented a new peptide-specific sampling and scoring protocol, termed SP-PEP, to improve the docking accuracy level; Page 1698, Column 2, Paragraph 4: Finally, in a separate experiment, the scaling factor to the ligand−atom van der Waals (vdW) radius was applied only during the rough scoring stage. The values for this new scaling factor were 0.2, 0.4, 0.6, and 0.8). The three dimensional structure, composed of van der Waals radii, was scaled to predefined decimal values (i.e. decimals are fractions which are ratios) applied to each atom within the model. Claim 9 recites the limitations of claim 4 directed to a method. It would have been obvious to one of ordinary skill in the art at the time of the effective filing date to combine Tubert-Brohman et al. with Gao et al. and Jiang et al. because Tubert-Brohman et al. teach novel methods of modeling protein binding with increased accuracy (Page 1697, Column 1, Paragraph 2: We implemented a new peptide-specific sampling and scoring protocol, termed SP-PEP, to improve the docking accuracy level), which is a major focus of both Gao et al. and Jiang et al. (see reason to combine Gao et al. and Jiang et al.). Tubert-Brohman et al. also teach their methods are applicable to drug active site discovery (Page 1689, Column 2, Paragraph 2: The Glide SP algorithm is computationally efficient, generally yielding results in 15 s for a typical drug-like molecule), which is also a major focus of both Gao et al. and Jiang et al. (see reason to combine Gao et al. and Jiang et al. above). Therefore, it would have been obvious to someone of ordinary skill in the art at the time of the effective filing date to combine the methods from the references indicated above. Furthermore, one of ordinary skill in the art would predict that the methods taught by Tubert-Brohman et al. could be readily combined with the methods of Jiang et al. and Gao et al. with a reasonable expectation of success because both are within the same technical field - modeling and making predictions based on three dimensional protein structure related to binding sites. Accordingly, 1-10 taken as a whole would have been prima facie obvious before the effective filing date and are rejected under 35 U.S.C. 103. Double Patenting No double patenting was identified. Conclusion No Claims are allowed. No 101 rejection was made because the claims were directed to statutory categories and independent claims 1 and 6 where not found to recite Judicial Exceptions. These independent claims recite limitations related to methods and a device to detect a pathogenic mutation and drug active site within the three dimensional structure of a protein. These limitations were not found to recite an abstract idea or natural phenomenon. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BLAKE H ELKINS whose telephone number is (571)272-2649. The examiner can normally be reached Monday-Friday 8-5PM. 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, Karlheinz 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. 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. /B.H.E./Examiner, Art Unit 1687 /Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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Prosecution Timeline

Aug 29, 2022
Application Filed
Jun 04, 2026
Non-Final Rejection mailed — §103, §112, §DP (current)

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Prosecution Projections

1-2
Expected OA Rounds
100%
Grant Probability
99%
With Interview (+0.0%)
4y 1m (~3m remaining)
Median Time to Grant
Low
PTA Risk
Based on 1 resolved cases by this examiner. Grant probability derived from career allowance rate.

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