Prosecution Insights
Last updated: August 17, 2026
Application No. 18/171,127

STABLE STRUCTURE SEARCH SYSTEM, STABLE STRUCTURE SEARCH METHOD, AND COMPUTER-READABLE RECORDING MEDIUM STORING STABLE STRUCTURE SEARCH PROGRAM

Non-Final OA §101§102§103§112
Filed
Feb 17, 2023
Priority
Jun 16, 2022 — JP 2022-097375
Examiner
SMITH, JENNIFER JOY
Art Unit
Tech Center
Assignee
Fujitsu Limited
OA Round
1 (Non-Final)
Grant Probability
Favorable
1-2
OA Rounds

Examiner Intelligence

Grants only 0% of cases
0%
Career Allowance Rate
0 granted / 0 resolved
-60.0% vs TC avg
Minimal +0% lift
Without
With
+0.0%
Interview Lift
resolved cases with interview
Typical timeline
Avg Prosecution
21 currently pending
Career history
15
Total Applications
across all art units

Statute-Specific Performance

§101
30.8%
-9.2% vs TC avg
§103
29.7%
-10.3% vs TC avg
§102
15.4%
-24.6% vs TC avg
§112
18.7%
-21.3% vs TC avg
Black line = Tech Center average estimate • Based on career data from 0 resolved cases

Office Action

§101 §102 §103 §112
DETAILED ACTION Notice of Pre-AIA or AIA Status 1. 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 2. Claims 1-12 are currently pending and under exam herein. Claims 1-12 are rejected. Priority 3. Claimed benefit of foreign priority to the prior Japanese Patent Application No. 2022-97375, filed on 16 June 2022, is acknowledged. A certified copy of the priority document has been received. In this action, all claims are examined as though they had an effective filing date 16 June 2022. 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 4. The information disclosure statements (IDSs) submitted on 17 February 2023, 18 January 2024, and 14 November 2025 are being considered by the examiner. Note that the IDSs submitted 25 January 2024 and 09 February 2024 were not considered as they are duplicates of the IDS submitted 18 January 2024. Drawings 5. The drawings submitted 17 February 2023 are accepted and being considered by the examiner. 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. Claims 1-12 are 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. Claims 1, 11, and 12 include a limitation in parentheticals and it is unclear if that is intended to be a limitation in the claim or not. For the purpose of examination and with broadest reasonable interpretation, the limitation in the parentheticals will not be considered as limitations in the claims. Claims 2-10 are rejected because they depend from claim 1 and do not resolve the dependency issue from claim 1. 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. 6. Claims 1-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Step 2A, Prong 1 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: Claims 1, 11 and 12 recites: calculating, in a model in which N particles (N is an integer equal to or greater than two) arranged in a shape of a row are arranged in a lattice space, coordinates in the lattice space of an i+1-th particle in the row, by using the coordinates in the lattice space of an i-th particle in the row, and state variables represented by relative coordinates in the lattice space of the i-th particle and the i+1-th particle Claims 1, 11 and 12 recites: computing a value of energy of the model, based on the coordinates in the lattice space of each of the N particles, every time the state variables are altered Claims 1, 11 and 12 recites: specifying the state variables with which the value of the energy has a local minimum value Claim 2 recites: the stable structure search system according to claim 1, the processing further comprising performing search processing that includes altering any one variable among N-1 variables included in the state variables Claim 3 recites: the stable structure search system according to claim 1, wherein the relative coordinates are the coordinates of the i+1-th particle when the i-th particle is arranged at an origin in the lattice space Claim 4 recites: The stable structure search system according to claim 3, wherein the calculating of the coordinates includes calculating the coordinates of the i+1-th particle when the state variables are altered, based on the altered state variables Claim 5 recites: The stable structure search system according to claim 4, wherein the calculating of the coordinates includes calculating the coordinates of each of an i+2-th particle to an N-th particle, by assuming that each of the i+2-th particle to the N-th particle moves in parallel along with a movement of the i+1-th particle Claim 6 recites: The stable structure search system according to claim 2, wherein the computing of the value of the energy of the model includes computing the value of the energy based on an interaction between the N particles, based on the coordinates in the lattice space of each of the N particles Claim 7 recites: The stable structure search system according to claim 6, wherein the energy includes at least any one of: an energy according to angles between the N particles, an energy according to dihedral angles between the N particles, an energy according to a repulsive force or an attractive force between the N particles, and an energy according to a distance between the particles at two ends when the N particles have a cyclic structure Claim 8 recites: The stable structure search system according to claim 5, wherein the computing of the value of the energy of the model includes computing a difference between the energy after the state variables are altered and the energy before the state variables are altered Claim 9 recites: The stable structure search system according to claim 6, wherein the search processing includes determining that alteration of the state variables is permitted when the difference computed by the computing satisfies a predetermined condition Claim 10 recites: The stable structure search system according to claim 9, wherein the specifying of the state variables includes specifying, from among the state variables altered within a range of a predetermined number of updates, the state variables when determined by the search processing to be alterable and with which the energy that corresponds to the state variables has the local minimum value. The limitations regarding ‘calculating coordinates in the lattice space’, ‘computing a value of energy of the model’ and ‘computing a difference between in energy before and after altering state variables’ are verbal equivalents that describe a mathematical calculation that is performed as the limitation and are so simple that they could be performed in the human mind or with pen and paper. Therefore, these limitations fall under the "Mathematical concepts" and "Mental processes" groupings of abstract ideas. The remaining limitations for ‘specifying the state variables’, ‘altering any one variable’ and ‘determining that alteration of the state variable is permitted based on the data’, are generically recited data analysis steps that can be practically performed in the human mind because the human mind is capable of identifying relevant information, comparing values, and determining information from other values. The limitations in claims 3 and 7 that further limit ‘the position of the coordinates’ or ‘the source or type of energy computed’ are part of the abstract idea because they merely further limit the Mathematical calculations but don’t change their position as ‘Mathematical concepts’. While claims 1, 11 and 12 recite performing some aspects of the analysis with a processor or a computer, there are no additional limitations that indicate that this processor or computer requires anything other than carrying out the recited mental process or mathematical concept 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 1-12 recite an abstract idea (Step 2A, Prong 1: YES). Step 2A, Prong 2 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 or insignificant extra-solution activity. Specifically, the claims recite the following additional elements: Claim 1 recites: a memory Claim 1 recites: a processor coupled to the memory, the processor being configured to perform processing Claim 11 recites: implemented by a computer Claim 12 recites: A non-transitory computer-readable recording medium Claim 12 recites: storing a stable structure search program for causing a computer to perform processing There are no limitations that indicate that the processor or computer requires anything other than a generic computing system. The configuration of the generic computer system (i.e. the terminal device) is described in the specification (para. 0097). It is further disclosed in the specification that the Ising device may be similar to the hardware configuration of the terminal device or it may be similar to the hardware configuration of a so-called quantum computer (para. 0105). As the use of the quantum computer is optionally included, it is not considered to be a necessary component of the claimed system and method. 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. The limitations for storing a stable structure search program is insignificant extra-solution activity that does not provide a practical application because it is tangentially related to the invention. As set forth in MPEP section 2106.05(g), the courts have recognized computer implementation as insignificant extra-solution activity. The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 1-12 are directed to an abstract idea (Step 2A, Prong 2: NO). Step 2B 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). The claims do not include 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 or well-understood, and conventional activity. As discussed above, there are no additional limitations to indicate that the claimed processor or computer requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As set forth in MPEP § 2106.05(d), storing and retrieving information in memory are well-understood, routine, conventional computer functions as recognized by 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. 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. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-12 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. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. 7. Claims 1-4, 6-7 and 9-12 are rejected under 35 U.S.C. 102 (a)(1) as being unpatentable over Babej et al. (arXiv, 2018, p. 1-12; 1/18/2024 IDS document), as evidenced by Miyazawa et al. (1985, Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macro-molecules, 18(3):534-552. The italicized text corresponds to the instant claim limitations. Regarding claims 1, 11 and 12, Babej et al. teaches a method of coarse-grained 3-D lattice protein folding by constructing a hybrid algorithm for protein folding executed on a quantum processor via cloud access (p. 2, col. 1, para. 3; p. 10, col. 1, para. 2; a stable structure search system comprising: a memory; and a processor coupled to the memory, the processor being configured to perform processing (claim 1); a stable structure search method implemented by a computer (claim 11); a non-transitory computer-readable recording medium storing a stable structure search program for causing a computer to perform the disclosed processing (claim 12). Regarding claims 1, 11 and 12, Babej et al. discloses conducting a 3D lattice folding experiments using an 8 amino acid snippet of Trp-Cage, a well-studied mini-protein. Babej et al. further discloses a developing a coarse-grained lattice model using a quantum annealing device to decode a given solution string into a lattice protein fold using an Ising-type Hamiltonian system. Babej et al. further discloses that an injective mapping is constructed between the set of all possible lattice protein folds and the set of binary strings/spins represented by a sequence of qubits (i.e. state variables) in the machine. Babej et al. further teach that the position of each amino acid in the lattice is dependent on the position of the amino acid before it in the sequence (i.e. the i+1-th amino acid depends on the position of the i-th amino acid). (p. 10, col. 1, para. 2; p. 2, col. 1, para. 4 – col. 2. Para. 3; Fig. 7C, Fig. 6A; p. 3, col. 1, para. 4 – p. 5, col. 2, para. 3; calculating, in a model in which N particles (N is an integer equal to or greater than two) arranged in a shape of a row are arranged in a lattice space, coordinates in the lattice space of an i+1-th particle in the row, by using the coordinates in the lattice space of an i-th particle in the row, and state variables represented by relative coordinates in the lattice space of the i-th particle and the i+1-th particle). Regarding claims 1, 11 and 12, Babej et al. discloses that in analyzing the search space using the Hamiltonian algorithm, for each conformation searched, the energy of the protein fold is calculated as the sum of interaction energies between adjacent non-covalently bound amino acids defined by a contact potential. Babej et al. further discloses that this is done by calculating Miyazawa and Jernigan (MJ) interaction strengths for the interacting amino acid pairs in the depicted lattice folds and that the goal of searching various conformations is to obtaining a conformation solution with ground state energy. Babej et al. further disclose using the protein folding algorithm and a quantum processor, to perform multiple conformation iterations obtain the lowest energy conformation of the lattice protein corresponding to ground state energy. As per Babej et al., this involves constructing an injective mapping between the set of all possible lattice protein folds and the set of binary strings represented by a sequence of qubits in the machine to uniquely decode a given solution string into a lattice protein fold (p. 2, col. 1, para. 3 – p. 3, col. 2, para. 2; p. 10, col. 2, para. 2; P. 10, col. 1, para. 2; Fig. 6A; computing a value of energy of the model, based on the coordinates in the lattice space of each of the N particles, every time the state variable are altered). Regarding claims 1, 11 and 12, Babej et al. further discloses constructing the energy landscape of for the Ising system such that the valid, lowest energy conformation of the lattice protein corresponds to the ground state of the system. Babej et al. further discloses specifying the ground state lattice folds for the Trp-Cage peptide (i.e. combination of vector directions that had the local minimum energy). Babej et al. displays the state variables with which the value of energy is ground state in Figure 6A (Fig. 6A; p. 2, col. 2, para. 3; specifying the state variables with which the value of the energy has a local minimum value). Regarding claim 2, in the method of Babej et al. state variables are coordinates/positions of amino acids. Babej et al. discloses mapping lattice proteins to binary by imposing a binary coordinate system onto a cubic 3D lattice using a set of globally defined directions called turns. Babej et al. further discloses doing this by first fixing the initial amino acid as a point of origin and then performing search processing to sequentially position each subsequent amino acid in relation to the first using a Hamiltonian construction (therefore N-1 coordinates are established by search processing for a protein of N amino acids). Babej et al. discloses that this method involves searching a solution space to optimize the combination of turns to achieve a ground state solution (p. 2, col. 2, para. 4 – p. 3, col. 2, para. 2; Fig. 1; the stable structure search system according to claim 1, the processing further comprising performing search processing that includes altering any one variable among N-1 variables included in the state variables. Pertaining to claim 6, Babej et al. discloses that the Hamiltonian approach includes a component Hpair that accounts for the interaction between non-bonded amino acids that are adjacent on the lattice using the HP (hydrophobic-polar) or MJ (Miyazawa and Jernigan) interaction potential. Babej et al. discloses that the energy of the protein fold can be calculated as the sum of interaction energies between adjacent non-covalently bound amino acids defined by the contact potential (p. 3, col. 2, para. 2;p. 2, col. 1, para. 5 – col. 2, para. 1; the stable structure search system according to claim 2, wherein the computing of the value of the energy of the model includes computing the value of the energy based on an interaction between the N particles, based on the coordinates in the lattice space of each of the N particles). Regarding claim 7, As evidenced by Miyazawa et al., the MJ matrix utilized By Babej et al. to compute the energy encodes both attractive (e.g., placing hydrophobic amino acids next to each other) and repulsive energies (e.g. forcing polar and nonpolar residues into contact). Miyazawa et al. discloses by the method of MJ interaction potential, hard-core repulsions are explicitly taken into account in a lattice model and short-range attractive interactions are included as effective contact energies between residues (p. 536, col. 1, para. 3; the stable structure search system according to claim 6, wherein the energy includes at least any one of: an energy according to angles between the N particles, an energy according to dihedral angles between the N particles, an energy according to a repulsive force or an attractive force between the N particles, and an energy according to a distance between the particles at two ends when the N particles have a cyclic structure). Pertaining to claim 9, Babej et al. discloses that the turn-based approach is based on optimization of a ground state that minimizes the total Hamiltonian energy through combinatorial optimization of 4 different subcomponents of the total energy in this equation: H q = H b a c k q + H r e d u n q +     H o l a p q +     H p a i r q     (where H is total energy, and q represents coordinates of the system); therefore, the alteration state is permitted when combinatorial optimization reaches a state that minimizes total Hamiltonian energy (Equation 3; p. 2, col. 2, para. 4 – p. 3, col. 2, para. 2; Fig. 6A; p. 2, col. 2, para. 3 the stable structure search system according to claim 6, wherein the search processing includes determining that alteration of the state variables is permitted when the difference computed by the computing satisfies a predetermined condition). [AltContent: textbox (Figure 1, Equation 1 of Babej et al. showing the finite number of attempts in optimizing the ground state. There are a finite number of configuration choices. q is configuration and N is number of amino acids in the protein.)] PNG media_image1.png 62 361 media_image1.png Greyscale Pertaining to claim 10, Babej et al. discloses that the turn-based approach is based on optimization of a ground state that minimizes the total Hamiltonian energy through combinatorial optimization of 4 different subcomponents of the total energy in this equation: H q = H b a c k q + H r e d u n q +     H o l a p q +     H p a i r q     (where H is total energy, and q represents coordinates of the system); therefore, the alteration state is permitted when combinatorial optimization reaches a state that minimizes total Hamiltonian energy. Using this approach, the configuration q represents a series of binary choices because there is a fixed search space and because of lattice constraints (e.g. many bit sequences are invalid because they result in self-intersection). Babej et al. discloses equation 1 (Figure 1 of this office action) that shows that there are a specific, calculable number of individual attempts within the sequence of length N (in this case N=8) (Equations 1 and 3; p. 2, col. 2, para. 4 – p. 3, col. 2, para. 2; Fig. 6A; the stable structure search system according to claim 9, wherein the specifying of the state variables includes specifying, from among the state variables altered within a range of a predetermined number of updates, the state variables when determined by the search processing to be alterable and with which the energy that corresponds to the state variables has the local minimum value). Regarding claim 3, Babej et al. discloses that a lattice protein is a path in the lattice graph and it is also specified as a sequence of edge directions with an initial point that is fixed as the point of origin. (p. 2, col. 2, para. 4; Fig. 1; the stable structure search system according to claim 1, wherein the relative coordinates are the coordinates of the i+1-th particle when the i-th particle is arranged at an origin in the lattice space). Pertaining to claim 4, Babej et al. discloses that the position of the first amino acid is fixed in a lattice and the relative positions of subsequent amino acids in the peptide are calculated based on the equation shown in Figure 1 of this office action (corresponding to equation 1 in Babej et al.) and based on equation 3 of Babej et al. By these equations, coordinate system q includes the position of each amino acid in the lattice and searching the solution space involves optimizing the combination of the coordinates for each amino acid (p. 2, col. 2, para. 4 – p. 3, col. 2, para. 2; Fig. 1, equation 1, each amino acid the stable structure search system according to claim 3, wherein the calculating of the coordinates includes calculating the coordinates of the i+1-th particle when the state variables are altered, based on the altered state variables. Claim Rejections - 35 USC § 103 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action: A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made. 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. 8. Claims 5 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Babej et al. (arXiv, 2018, p. 1-12; 1/18/2024 IDS document), as evidenced by Miyazawa et al. (1985, Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macro-molecules, 18(3):534-552), as applied to claims 1-4, 6-7, and 9-12 above, and further in view of Covell et al. (1992, Proteins: structure, function and genetics, vol. 14, p. 409-420). The instant claim limitations are italicized. The limitations of Claims 1-4, 6-7 and 9-12 have been taught by Babej et al. above. Regarding claim 5, Babej et al. discloses that for verification purposes, the correct lattice fold determined using the Hamiltonian algorithm was modeled using a classical Monte-Carlo solver on classical hardware. As evidenced by Covell et al., Monte Carlo methods for generating folded chains of amino acid sequences include allowed chain transitions for the lattice model that include those that preserve the relationship of the i + 1-th amino acid and the i + 2-th amino acid. Covell et al. further provides the example of pivot move transitions where a contiguous group of chain elements is moved as a rigid body around a central chain element (Babej et al. p. 10, col. 1, para. 2; Covell et al., p. 410, col. 1, , para. 2 – col. 2, para. 1; Fig. 1e ; the stable structure search system according to claim 4, wherein the calculating of the coordinates includes calculating the coordinates of each of an i+2-th particle to an N-th particle, by assuming that each of the i+2-th particle to the N-th particle moves in parallel along with a movement of the i+1-th particle). An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Babej et al. teaches the application of both methods separately in the same study and specifically teaches that Monte-Carlo was used for validation, suggesting it is recognized as a well-established method for predicting peptide structure that is orthogonal to the Hamiltonian approach (p. 10, col. 1, para. 2). Corvell et al. disclose that the Monte-Carlo method provides folding structures similar to native-like chain topologies (p. 419, col. 1, para. 2-3). Therefore, one of ordinary skill in the art would have been motivated combine the two different methods into a hybrid approach to take advantages of the benefits of each approach. Furthermore, one of ordinary skill in the art would predict that the methods taught by Babej et al. could be combined with a reasonable expectation of success because they both pertain to predicting peptide structure using a lattice approach and they have both been applied to predict the structure of the same peptide and yielded similar results. The invention is therefore prima facie obvious. Pertaining to claim 8, Babej et al. teaches obtaining the lowest energy confirmation of the lattice protein and that the energy landscape is constructed for the Ising system such that the valid, lowest energy conformation of the lattice protein corresponds to the ground state of the system. According to Babej et al., this is done using pseudo-Boolean expressions. Babej et al. does not explicitly teach comparing the energy of different altered states in the energy landscape before the final confirmation with the lowest energy is selected, but this is implied in the method since multiple energies are calculated and the lowest needs to be selected and simple subtraction is the easiest way to compare the energies (p. 2, col. 1, para. 3; p. 2, col. 2, para. 3; the stable structure search system according to claim 5, wherein the computing of the value of the energy of the model includes computing a difference between the energy after the state variables are altered and the energy before the state variables are altered). E-mail Communications Authorization 9. Per updated USPTO Internet usage policies, Applicant and/or applicant's representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300): "Recognizing that Internet communications are not secure, / hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. / understand that a copy of these communications will be made of record in the application file." Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273- 8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03. Inquiries 10. Any inquiry concerning this communication or earlier communications from the examiner should be directed to JENNIFER J SMITH whose telephone number is (571)272-7801. The examiner can normally be reached Monday-Friday 7:30 AM - 4:00 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. /J.J.S./Examiner, Art Unit 1685 /OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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Prosecution Timeline

Feb 17, 2023
Application Filed
Jul 15, 2026
Non-Final Rejection mailed — §101, §102, §103
Aug 03, 2026
Examiner Interview Summary
Aug 03, 2026
Applicant Interview (Telephonic)

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