DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Herein, “the previous Office action” refers to the Final Rejection filed on 7/22/2025.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/19/2026 has been entered.
Priority
As detailed on the Filing Receipt filed 3/8/2021, the instant application claims priority to as early as 11/8/2017. At this point in prosecution, all claims are accorded the earliest claimed priority date.
Claim Status
Claims 2, 6-7, 14 and 16 are canceled.
Claims 1, 3-5, 8-13 and 15 are pending, and under examination.
Withdrawn Objections/Rejections
The objection to claims 1 and 15 is hereby withdrawn in view of Applicant’s amendment of the claims to resolve a minor grammatical informality.
The rejection of claim 14 under 35 USC § 101, as being directed to nonstatutory subject matter, is hereby withdrawn in view of Applicant’s cancellation of the claim.
Claim Interpretation
This section documents the Examiner’s interpretation of recited preamble language under prosecutorial standards.
The preambles of claims 1 and 15 characterize claimed subject matter as “for molecular simulations” (claim 1, line 2; claim 15, lines 2-3). This phrase does not appear in the body of either claim, and its appearance in each preamble appears to indicate an intended use or purpose for the claimed invention.
The courts have ruled that “where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation” (Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997). Here the preambles appear to merely indicate an intended use or purpose for elements of the claims, and the cited phrase is not considered to be structurally limiting. See MPEP 2111.02 § II.
Dependent claims 17-18 specify that the molecular simulations include protein folding or protein ligand docking. These claims are viewed as merely narrowing the scope of the indicated purpose or intended use, which is likewise not considered to further limit the structure of the claimed invention.
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.
Claims 1, 3-5, 8-13 and 15 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 new grounds of rejection presented herein were necessitated by Applicant’s amendment of the claims (filed 1/19/2026).
With respect to claims 1, 15 and dependents therefrom, the scope of the recited limitation “identifying movement of the structure information of the protein based on changes in color variations and intensity in said fixed-sized encoded representation” (claim 1, lines 28-30; claim 15, lines 35-37) is uncertain. Both of claims 1 and 15 require that said representation comprises saturation levels that correspond to various color channels and encode protein structural information, while claim 15 further specifies that the representation is a tensor or image. Said representation is a single data structure, not an ordered series of data structures.
It is unclear how the color variations and intensities (i.e., the saturation levels representing these) in this single representation can undergo changes, or convey movement of encoded structural information. For the purposes of further prosecution herein, the recited limitation is interpreted as “identifying movement of the structure information of the protein based on changes in color variations and intensity between a plurality of fixed-sized encoded representations”.
For the above reasons, the claims are indefinite.
Claim Rejections - 35 USC § 101
35 USC § 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, 3-5, 8-13 and 15 are rejected under 35 USC § 101 because the claimed invention is directed to non-statutory subject matter. This rejection is maintained from the previous Office action and has been revised to address the amended claims (filed 1/19/2026).
"Claims directed to nothing more than abstract ideas, natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I).
Abstract ideas include mathematical concepts (including formulas, equations and calculations), and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than an abstract idea.
Step 1: The Four Categories of Statutory Subject Matter (MPEP 2106.03)
The claims are directed to methods (claims 1, 3-5 and 8-13) and a computer system (claim 15), which fall under categories of statutory subject matter.
Step 2A, Prong One: Whether the Claims Set Forth or Describe a Judicial Exception (MPEP 2106.04 § II.A.1)
‘Mathematical concepts’ are relationships between variables and numbers, numerical formulas or equations, or acts of calculation, which need not be expressed in mathematical symbols (MPEP 2106.04(a)(2) § I). The claims recite elements which encompass mathematical concepts, at least under their broadest reasonable interpretation, including:
“extracting protein secondary structure information from a three-dimensional structure of the protein using a Ramachandran plot… based on torsion angles between an alpha carbon, an amino group, and a carboxyl group of [each] amino acid” (claim 1) and “extracting protein secondary structure information from a primary amino acid sequence using a Ramachandran plot… based on a torsion angle between C-N-CA-C or N-CA-C-N atoms in the amino acid sequence” (claim 15), i.e., calculating information from coordinates or amino acid identities using a plotted ruleset;
“expressing… tertiary structure information using a distance matrix… wherein the tertiary structure information is based on the distance between atoms in the three-dimensional structure” (claims 1 and 15), i.e., calculating distances using coordinate data;
“encoding both said… secondary structure information and… tertiary structural information [into a tensor or an image]” (claims 1 and 15), e.g., rendering information as a mathematical expression;
“combining all the color channels into a single representation” (claim 1) wherein “said representation is an image or tensor” (claim 4), and “combining all said color channels into a single tensor or image” (claim 15), e.g., rendering information as a mathematical expression;
“formatting said representation into a fixed-sized encoded representation” (claim 1) and “formatting said tensor or said image into a fixed-sized encoded representation” (claim 15), e.g., calculating an output of fixed size from an input tensor;
“resizing said representation to produce said fixed-sized encoded representation” (claim 8), i.e., scaling input data to produce output of fixed size;
“resizing… includes the use of bicubic interpolation” (claim 9), i.e., scaling an input using a bicubic interpolation algorithm; and
“analyzing said fixed-sized encoded representation using pattern recognition by a convolutional neural network” (claim 12), e.g., calculating an output from an input tensor using a convolutional neural network algorithm.
The recited acts of calculation constitute mathematical concepts.
‘Mental processes’ are processes that can be performed in the human mind at least with use of a physical aid, e.g., a slide rule or pen and paper (MPEP 2106.04(a)(2) § III). The recited acts of calculation are practicably performable in the human mind, at least under the broadest reasonable interpretation, rendering them as mental processes. The claims further recite the following element that likewise encompasses mental processes, at least under the broadest reasonable interpretation:
“displaying said fixed-sized encoded representation, wherein said… representation comprise[s] color patterns at various levels of granularity” (claims 1 and 15), i.e., presenting results of data manipulation steps encompassing abstract ideas; and
“identifying movement of the structure information of the protein based on changes in color variations and intensity [between a plurality of] fixed-sized encoded representation[s]” (claims 1 and 15), i.e., interpreting information.
The human mind is capable, with physical aid (e.g., pen and paper), of visually rendering a tensor of output values. The above elements thus encompasses embodiments of sufficient simplicity for consideration as mental processes.
Further claim elements delimit embodiments of the above mental processes and mathematical concepts but do not alter their characterization as such, including:
the encoded representation is “for molecular simulations” (claims 1 and 15), wherein “the molecular simulations include protein folding or protein ligand docking” (claims 17-18);
“each of said… secondary structure information is assigned a different color as defined by saturation levels of a red color channel, a blue color channel, and a green color channel” (claims 1 and 15), i.e., numeric values;
“a α-helix is assigned to red, a β-strand assigned to blue, a Polyproline PII-helix is assigned to magenta, a γ’-turn is assigned to yellow, a γ-turn is assigned to cyan, a cis-peptide bond is assigned to green, and an indeterminate structure is assigned to black” (claim 1);
“each of said… tertiary structural information is assigned a position in the distance matrix representing the distance between the alpha carbon atoms” (claims 1 and 15), i.e., a numeric value;
“said distance matrix is a squared matrix” (claim 3);
“said tensor includes a dimension defined by M x M x Z, where M is a number of amino acid residues in the protein and Z is a number of color channels used to encode said… information” (claim 5) and “said fixed-sized encoded representation is defined as [a] N x N x Z tensor, where N represents a new size of an image, and Z is a number of channels used to encode said… information” (claim 10), i.e., mathematical expressions have particular form and representative nature;
“said encoded representation further includes one or more additional protein information selected from… electromagnetic charge, residual energy, and hydrophobicity” (claim 11);
“said convolutional neural network analyzes separately each of said color channels of said fixed-sized encoded representation using a convolutional 2D filter prior to combining each of said channels into a single representation” (claim 13), i.e., the convolutional neural network algorithm sequentially applies a matrix to subsets of input data; and
“the protein secondary structure is selected from… an α helix, a β-strand, a Polyproline PII-helix, a γ’-turn, a γ-turn, a cis-peptide [bond], and [an] indeterminate structure” (claim 15).
Mathematical concepts and mental processes are enumerated groupings of abstract ideas (MPEP 2106.04(a)(2) §§ I and III). Hence, the claims recite elements that, individually and in combination, constitute an abstract idea. The claims must therefore be examined further to determine whether they integrate this abstract idea into a practical application (MPEP 2106.04(d)).
Step 2A, Prong Two: Whether the Claims Contain Additional Elements that Integrate the Judicial Exception(s) into a Practical Application (MPEP 2106.04 § II.A.2)
The claims recite the following additional element, which recites a generic computer implementation of the claimed method:
“A computer system… comprising: one or more processors and a memory storing at least one program for execution… comprising instructions for” (claim 15) performance of claimed method functions.
The claims do not describe any specific computational steps by which the computer system performs or carries out functions drawn to the abstract idea, nor do they provide any details of how specific structures of the computer system are used to implement these functions. The claims state nothing more than that a computer system performs functions drawn to the abstract idea, and are therefore mere instructions to apply the abstract idea using a generic computer. As such, the claims do not integrate the abstract idea into a practical application (see MPEP 2106.04(d) § I and 2106.05(f)).
No further additional elements are recited.
When the claims are considered as a whole: they do not improve the functioning of a computer, other technology, or technical field (MPEP 2106.04(d)(1) and 2106.05(a)); they do not apply the abstract idea to effect a particular treatment or prophylaxis for a disease or medical condition (MPEP 2106.04(d)(2)); they do not implement the abstract idea with, or in conjunction with, a particular machine (MPEP 2106.05(b)); they do not effect a transformation or reduction of a particular article to a different state or thing (MPEP 2106.05(c)); and they do not apply or use the abstract idea in some other meaningful way beyond linking the use of the abstract idea to a particular technological environment and/or field of use (i.e., computer graphics; MPEP 2106.05(e) and 2106.05(h)).
Therefore, the claims do not integrate the abstract idea into a practical application. See MPEP 2106.04(d) § I.
Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are directed to the abstract idea. Claims that are directed to an abstract idea must be examined further to determine whether the additional elements besides the abstract idea render the claims as significantly more than the abstract idea. Additional elements besides the abstract idea may constitute inventive concepts that are sufficient to render the claims as significantly more (MPEP 2106.05).
Step 2B: Whether the Claims Contain Additional Elements that Amount to an Inventive Concept (MPEP 2106.05)
Mere instructions to apply an abstract idea using a computer are, when considered individually, insufficient to constitute an inventive concept that would render the claims significantly more than said abstract idea (see MPEP 2106.05(f)).
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a particular technological environment and/or field of use (i.e., computer graphics). See MPEP 2106.05(h).
Therefore, the claims do not provide an inventive concept and/or significantly more than the abstract idea itself. See MPEP 2106.05.
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Response to Arguments - Claim Rejections Under 35 USC § 101
In the Remarks filed 1/19/2026, Applicant traverses the rejection under 35 USC § 101 and presents supporting arguments.
Applicant notes that structural comparison of proteins is a critical aspect of multiple research problems, and states that structure-based function prediction often outperforms sequence-based methods (pg. 6, para. 7).
The claimed method graphically encodes protein structural information, and does not include steps of comparing protein structures or predicting protein function. The utility of prospective applications of a claimed invention is not germane to eligibility of the claimed invention itself under § 101. Integration of judicial exceptions into a practical application, or provision of an inventive concept sufficient to render the claims as significantly more, must be achieved by recited additional elements. Hence, this argument regarding prospective applications is found unpersuasive.
Applicant describes various features and operations of the claimed invention, and notes that understanding protein structural formation during folding and ligand binding may be crucial components for drug design (pg. 7, paras. 1-3).
The claimed invention does not include steps of drug design, and the utility of prospective applications of a claimed invention is not germane to eligibility of the claimed invention itself under § 101. Hence, this argument regarding prospective applications is found unpersuasive.
Applicant alleges that the claimed invention fulfills a need for a scalable method of encoding structural information into an easily searchable, computer-readable format as may be analyzed by machine learning methods (pg. 8, para. 2).
The mere fact that an invention processes particular information, or implements computational analysis of particular information via machine learning, is not equivalent to a practical application or inventive concept. See, e.g., Recentive v. Fox, 134 F.4th 1205, 1213-14 (Fed. Cir. 2025).
While the satisfaction of a long-felt, art-recognized problem (i.e., a ‘long-felt need’) is germane to obviousness of a claimed invention over prior art under § 103, it is not germane to eligibility of the claimed invention under § 101. Hence, the argument of need is found unpersuasive.
Applicant notes that the claimed invention identifies and presents protein structural information without the need for pairwise structural alignments or complicated homology calculations, and alleges that the encoded representation may significantly increase high-throughput techniques for predicting protein function (pg. 8, para. 2).
The claimed invention does not include steps of predicting protein function, and the referenced functional advantages (e.g., avoidance of pairwise alignment) regard prospective applications of the encoded representation rather than the claimed invention itself. The utility of prospective applications of a claimed invention is not germane to eligibility of the claimed invention itself under § 101. Hence, this argument regarding prospective applications is found unpersuasive.
Applicant alleges that the amended claims sufficiently apply and/or provide significantly more than the alleged abstract ideas. Specifically, Applicant alleges that the claimed combination of data pre-processing steps of rendering a Ramachandran plot, rendering a distance matrix, and joint encoding as an image) improves subsequent operation of a neural network related to molecular simulations and related protein structure evaluation and thus provides an inventive concept (pg. 8, para. 3).
The referenced data pre-processing steps encompass acts of mathematical calculation and organizing data, and a neural network is a series of mathematical functions. An inventive concept cannot be furnished by, albeit improved or unconventional, a judicial exception itself or a combination of judicial exceptions. See Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376 (Fed. Cir. 2016); RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327-28 (Fed. Cir. 2017). Hence, the argument of provision of improved neural network operation by combined data pre-processing steps is found unpersuasive.
For the above reasons, the arguments are found unpersuasive and the rejection is maintained with respect to the pending claims.
Conclusion
At this point in prosecution, no claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Theodore C. Striegel whose telephone number is (571)272-1860. The examiner can normally be reached Mon-Fri 12pm-8pm ET.
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/T.C.S./Examiner, Art Unit 1685
/JESSE P FRUMKIN/Primary Examiner, Art Unit 1685 February 7, 2026