DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 Feb 5 2025 has been entered.
Applicant’s response, filed Feb 5 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
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 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.
Claim Status
Claims 1-2, 4, 6-14, and 16-23 are pending.
Claims 3, 5, and 15 are canceled.
Claims 4, 6, 9-11, 13-14, 17, 19, and 21 are objected to.
Claims 1-2, 4, 6-14, and 16-23 are rejected.
Priority
The instant Application claims the benefit of domestic priority to US provisional application 62/635,536, filed Feb 26 2018.
Applicant's claim for the benefit of a prior-filed application, PCT/US2019/019530, filed Feb 26 2019, is acknowledged.
Accordingly, each of claims 1-2, 4, 6-14, and 16-23 are afforded the effective filing date of Feb 26 2018.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Feb 5 2025 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Claim Objections
The outstanding objections to the claims are withdrawn in view of the amendments submitted herein.
The claims are objected to because of the following informalities. The instant objection is newly stated and is necessitated by claim amendment.
Claim 4, line 3, recites “the second additional set values”, which should be amended to recite “the second additional set of values”.
Claim 6 should be amended to recite “The method of claim 1, further comprising”.
Claims 9, 11, 13, and 14 should be amended to recite “Gibbs free energy change”.
Claim 10, limitation 5, and claim 21, limitation 7, recite “a first differences”, which should be amended to recite “[[a]] first differences” or similar.
Claim 17 recites “comprising one or more analytical tests”. It is assumed that the claim should be amended to recite “further comprising performing one or more analytical tests”.
Claim 19 recites “a base protein”, which should be amended to recite “[[a]] the base protein”.
Claim Interpretation
In claims 6 and 11, under the broadest reasonable interpretation, “an amount of impact” in the limitation “comprising performing an analysis of variance or a t-test to determine an amount of impact of the candidate substitution on the Gibbs free energy” reads on the level of the statistical evaluation of the candidate substitution (i.e., whether or not the difference is statistically significant) rather than the magnitude in the difference of the measured Gibbs free energy, as is supported by the specification as published at least at [0064].
Claim Rejections- 35 USC § 112
35 USC § 112(b)
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 11-13, 17-18, and 21-23 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 instant rejection is newly stated and is necessitated by claim amendment.
Claims 11 and 13 recite “the amount of impact”. There is insufficient antecedent basis for the limitation because there is no previous recitation of determining the amount of impact. It is assumed that the limitations should have been amended to refer to the new language of determining that the candidate substitution produces a statistically significant effect on values of the Gibbs free energy change of the first group as recite in claim 10. The rejection may be overcome by clarifying the antecedent basis of the claims.
Claim 12 recites “determining, based at least partly on the comparison, that differences between the first amino acid sequence and a second amino acid sequence of the second protein and a third amino acid sequence of the third protein are less than a threshold number”. First, it is not clear which second protein of the “individual second proteins of the second group of the number proteins” recited in claim 10 is intended to be further limited, either each individual second protein or a specific one. Second, there is insufficient antecedent basis for the limitation because there is no previous recitation of a third protein. It is therefore not clear which third amino acid sequence of which third protein is intended to be used to determine the differences. It is assumed that the limitation should have been amended to refer to the new language of a subset of groupings as recited in claim 10, rather than the second and third proteins. The rejection may be overcome by clarifying the antecedent basis of the claim.
Claim 17 recites “one or more analytical tests to determine the first values for the Gibbs free energy change of the number of proteins and to determine the second values for the unfolding temperatures of the number of proteins”. Claim 18 recites “wherein the one or more analytical tests are performed to determine total molecular weight, heavy chain molecular weight, light chain molecular weight, percentage of heavy chain molecular weight relative to total molecular weight, percentage of light chain molecular weight relative to total molecular weight, or presence of a secondary structure”. It is not clear whether the claim intends to encompass an embodiment where one analytical test is used to determine both the Gibbs free energy change and the unfolding temperature values, as recited in claim 17, and one of the other recited values in claim 18, or if the claims intend to recite performing one analytical test for each different value. For compact examination, any analytical tests that can determine the claimed values will be considered relevant. The rejection may be overcome by clarifying how many analytical tests are required to be performed.
Claim 21 recites “A system comprising: one or more processors; and one or more non-transitory computer-readable media storing computer-readable instructions that, when executed by the one or more processors, perform operations comprising: obtaining, by one or more computing devices…”. It is not clear whether the one or more computing devices which is recited to perform the step directed to “obtaining” is intended to be part of the system or a computing device which is separate from the system. Because the claim recites that the “one or more non-transitory computer-readable media storing computer-readable instructions that, when executed by the one or more processors, perform operations comprising”, it is assumed that the one or more computing devices actually refers to the one or more processors of the system. The rejection may be overcome by either deleting the phrases “by (the) one or more computing devices” throughout the claim, or by clarifying the relationship between the system and the one or more computing devices. Claims 22-23 are rejected based on their dependency from claim 21.
Claim 21, 4th limitation, recites “the candidate substitution”. There is insufficient antecedent basis for this limitation because there is no previous recitation of a candidate substitution in the claim. The rejection may be overcome by amending the claim to recite “[[the]] a candidate substitution”. Claims 22-23 are rejected based on their dependency from claim 21.
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 1-2, 4, 6-14, and 16-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to methods and a system, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong 1
With respect to Step 2A, Prong 1, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong 1 evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claim 1: creating… a data set including the amino acid sequences, the first values, and the second values; and
determining… a candidate substitution indicating a modification of the amino acid sequence of the base protein at a respective position;
Independent claims 1, 10, and 21: determining… using the data set, a first additional data set that corresponds to a first group of the number of proteins that includes the candidate substitution, the first additional data set including first amino acid sequences of the first group of the number of proteins, a first set of the first values that correspond to the first group of the number of proteins, and a second set of the second values that correspond to the first group of the number of proteins;
determining… using the data set, a second additional data set that corresponds to a second group of the number of proteins that does not include the candidate substitution, the second additional data set including second amino acid sequences of the second group of the number of proteins, a first additional set of the first values that correspond to the second group of the number of proteins, and a second additional set of the second values that correspond to the second group of the number of proteins;
performing… comparisons between individual first positions of individual first amino acid sequences of the first group of the number of proteins and individual second positions of individual second amino acid sequences of the second group of the number of proteins;
determining… based on the comparisons, first differences between the individual first amino acid sequences and multiple groupings of the individual second amino acid sequences;
determining… based on the comparisons, second differences between the individual first amino acid sequences and the individual second amino acid sequences;
determining that a portion of the first differences is minimized with respect to the second differences for a subset of the groupings;
based on the determination that the portion of the first differences is minimized with respect to the second differences for the subset of groupings, generating… a modified data set that (i) represents individual groupings of the subset of groupings as a single protein having a first normalized value of the Gibbs free energy change and a second normalized value of the unfolding temperature based on the values of the Gibbs free energy change and the values of the unfolding temperatures of the respective proteins included in the individual groupings and (ii) indicates associations between individual second proteins of the second group of the number of proteins and one or more single proteins corresponding to one or more individual groupings;
determining… using the modified data set, additional differences between the first normalized values and the first additional set of values for the Gibbs free energy change that correspond to the second group of proteins;
determining… based at least partly on the additional differences, that the candidate substitution produces a statistically significant effect on values of the Gibbs free energy change of the first group; and
determining… based on the candidate substitution producing the statistically significant effect on the values of the Gibbs free energy change, one or more of the first group of the number of proteins that have a measure of stability that is greater than an additional measure of stability of the base protein.
Dependent claim 2: determining that at least one of yield or stability increases based at least partly on the statistically significant effect produced by the candidate substitution.
It is noted that the limitation is interpreted under the BRI as encompassing in silico assays or actions to determine the stability, as supported in the instant specification at least at [0028].
Dependent claim 4: determining… further differences between the second normalized values and the second additional set values for the unfolding temperatures that correspond to the second group of proteins.
Dependent claims 6 and 11: performing an analysis of variance or a t-test to determine an amount of impact of the candidate substitution on the Gibbs free energy.
Dependent claim 12: determining, based at least partly on the comparison, that differences between the first amino acid sequence and a second amino acid sequence of the second protein and a third amino acid sequence of the third protein are less than a threshold number.
Dependent claim 14: generating a user interface that includes at least one user interface element to capture a value for the Gibbs free energy with respect to the base protein.
Dependent claim 23: determining, based at least partly on an amount of impact on the candidate substitution on the Gibbs free energy change, that the candidate substitution has an effect on yield of the protein.
It is noted that the limitation is interpreted under the BRI as encompassing in silico assays or actions to determine the yield, as supported in the instant specification at least at [0028; 0065].
Dependent claims 8-9, 13, 19-20, and 22 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claims 8 and 19-20 further limit the candidate substitution of claims 1 and 10; claim 9 further limits determining how the candidate substitution produces the statistically significant effect in claim 1; claim 13 further limits determining the amount of impact to including determining a probability; and claim 22 further limits determining that the candidate substitution produces the statistically significant effect.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine whether a candidate substitution in a protein sequence has a statistically significant effect on the Gibbs free energy change in comparison with the base protein. Without further detail as to the methodology involved in “creating”, “determining”, “performing”, “generating”, and “comparing”, under the BRI, one may simply, for example, use pen and paper to record values and sequences of proteins to create a data set, sort the proteins into groups that have and do not have a candidate substitution, determine differences between proteins in different groups, determine minimized differences between subsets of the groupings of individual amino acid sequences, generate normalized values from those minimized groupings, use that information to determine that the candidate substitution has a statistically significant effect on the property, and determine values for the modified proteins using in silico processes. The step directed to “generating a user interface” in claim 14 is considered to encompass a mental action because one could write (i.e., capture) the value for the property of the protein on a piece of paper (i.e., a user interface). Some of these steps, such as “determining… that the candidate substitution produces a statistically significant effect”, and those recited in the dependent claims, require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0042; 0064; 0080; 00107; 00127].
Therefore, claims 1, 10, and 21, and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong 2
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong 2
With respect to the instant recitations, the claims recite the following additional elements:
Claim 1: physically expressing a number of proteins with amino acid sequences that have been modified to include one or more substitutions with respect to an amino acid sequence of a base protein;
performing one or more first analytical tests to determine first values for Gibbs free energy change of the number of proteins; and
performing one or more second analytical tests to determine second values for unfolding temperatures of the number of proteins.
Claims 10 and 21: obtaining… a data set that includes (i) amino acid sequences of a number of proteins that have been modified to include one or more substitutions with respect to an amino acid sequence of a base protein, (ii) first values for Gibbs free energy change of the number of proteins, and (iii) second values for unfolding temperatures of the number of proteins.
Dependent claims 7 and 16 further limits the base protein and the number of proteins physically expressed in claims 1 and 10 to being antibodies.
Dependent claim 17: comprising one or more analytical tests to determine the first values for the Gibbs free energy change of the number of proteins and to determine the second values for the unfolding temperatures of the number of proteins.
Dependent claim 18 further limits what values are determined by performing the one or more analytical tests of claim 17.
Claims 1, 10, and 21 and those claims dependent therefrom include non-abstract computing elements. Claim 1 includes one or more computing devices and one or more user interface elements. Claim 10 includes one or more computing devices. Claim 21 includes a system comprising: one or more processors; and one or more non-transitory computer-readable media storing computer-readable instructions that, when executed by the one or more processors, perform operations.
Considerations under Step 2A, Prong 2
With respect to Step 2A, Prong 2, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to insignificant extra-solution activity to the judicial exception, such as “physically expressing a number of proteins with amino acid sequences that have been modified at a number of positions with respect to an amino acid sequence of a base protein” and “performing” analytical tests in claim 1, perform activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim. The expressed proteins are not required to be acted upon by the remainder of the limitations, which are each performed by a computing device based on an actions performed on the in silico sequences of the proteins. Insignificant extra-solution activity does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Insignificant extra-solution activity is not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The limitations directed to additional non-abstract elements of a system as recited above do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)). Further, the computer system contains the recited instructions (i.e., software) that are used for performing the operations which are considered to recite judicial exceptions as described above. Thus, the limitations only generically link the use of the judicial exceptions to the technological environment of a computer.
The specification does not provide a clear explanation for how the additional elements improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the prior art review to Wrenbeck et al. (Current Opinion in Structural Biology, 2017, 45:36-44; previously cited) discloses that physically expressing a number of proteins, including antibodies, with amino acid sequences that have been modified at a number of positions with respect to an amino acid sequence of a base protein, and then examining the proteins under different conditions (such as temperature, etc.) to generate multiple fitness landscapes, and performing crystallography to determine the structure of proteins are insignificant extra solution activities that are routine, well-understood and conventional in the art. Said portions of the prior art are, for example: the abstract; p. 36, col. 1 through col. 2, par. 2 and par. 4; p. 38, col. 1-2; p. 39, col. 2, par. 1; p. 40, col. 1, par. 2-4, col. 2, par. 1 and par. 3; and Figures 1-2. Further, the prior art to Kumar et al. (Nucleic Acids Research, 2006, 34:D204-D206; newly cited) discloses ProTherm and ProNIT, which are thermodynamic databases for proteins where researchers can deposit thermodynamic data including changes in Gibbs free energy (ΔG), thermal denaturation, and secondary structure (abstract; Table 1). Kumar discloses that ProTherm contains 17,113 entries from 1497 scientific articles at the time of publishing (2006), demonstrating the widespread practice of measuring Gibbs free energy and unfolding temperatures. As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The insignificant extra solution activity as recited in the instant claims constitutes a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 1, 10, and 21 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (see MPEP 2106.06(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at [0067-0068]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 13, par. 4 through p.17, par. 2, Applicant submits that the claims are directed to a technological improvement and are patent eligible because the specific process recited in claim 1, for example, provides improvements in the field of identifying variants of proteins that have increased stability with respect to base proteins. Applicant points to the specification for support of this improvement, which discusses experimental data showing improved in determining significance and avoiding the synthesis of large numbers of proteins, thereby decreasing costs. Applicant submits that the claims provide a specific process for producing an unbalanced data set which is then practically applied by determining more stable variants. Applicant submits that even if some claim elements are directed to an abstract idea, when the claim elements provide a technological improvement, the Courts have found that the claims can still be directed to patent eligible subject matter, as in Enfish and McRO.
It is respectfully submitted that this is not persuasive. Applicant alleges that the method of comparing different subgroups of proteins to balance a dataset represents an improvement in identifying more stable protein sequences. However, steps directed to determining subgroups of proteins with and without the candidate substitution and minimized numbers of other substitutions (the unbalanced data set as submitted by Applicant) that provide the supposed improvement of identifying improved protein sequences in the instant claims are steps that are, themselves, the judicial exceptions and cannot therefore be a practical application of the judicial exception. The courts have made clear that a judicial exception is not eligible subject matter (Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)) if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, it is the additional elements (if any) in the claim that must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B. If there are no additional elements in the claim, then it cannot be eligible. It is submitted here that the instant claims do not include any additional elements that provide for a practical application. Rather, the “additional element” in the instant claims (see exemplary claim 1) includes only the step of “physically expressing a number of proteins” and “performing” first and second analytical tests. As set forth above, said steps operate in the claim as data gathering steps and do not integrate any of the recited judicial exceptions into a practical application, nor do the claims as a whole include any inventive concept beyond well-understood, routine and conventional steps.
Regarding the avoided costs of synthesizing large numbers of proteins, it is noted that Applicant’s arguments are not commensurate with the scope of the claims. Claim 1, for example, requires “physically expressing a number of proteins with amino acid sequences” and “performing” first and second analytical tests on the proteins. The claims do not recite any limited number of proteins being synthesized and tested, and embodies such acts being performed on both very small and very large numbers of proteins. Additionally, the claims require only that the number of proteins have “amino acid sequences that have been modified to include one or more substitutions”. An embodiment where only one amino acid is modified per protein does not realize the improvement submitted by Applicant and provided by a smaller dataset where multiple substitutions occur per protein. Therefore, the claims recite embodiments which do not provide any avoided costs in comparison with existing technology.
The claims are also found not to be analogous to Enfish and McRO. In both Enfish and McRO, the additional elements of the claims provided for an improvement in the functioning of a computer, which integrated the recited judicial exception into a practical application. For the reasons explained above, the instant claims do not recite additional elements which provide for an improvement or any other practical application. The instant additional elements in the claim serve only data gathering functions or recite the application of the judicial exception on a generic computer.
At p. 17, par. 3 through p. 21, par. 2, Applicant submits that the claim elements characterized as abstract ideas are actually for multiple reasons. First, at p. 18, par. 2, Applicant submits that claim 1 recites at least some limitations, such as those directed to “physically expressing” proteins and “performing” analytical tests, which do not recite abstract ideas. Applicant submits that generating an initial data set from these specific measurements of protein stability enables the unbalanced data set described above to be produced later in amended claim 1. Second, at p. 18, par. 3 through p. 19, par. 2, Applicant submits that generating the modified, unbalanced data set of amended claim 1 through transforming multiple other data sets does not actually recite mathematical concepts, but involves the use of mathematical concepts, similarly to Examples 38-39 in the USPTO’s Subject Matter Eligibility Examples. Third, at p. 20, par. 1 through p. 21, par. 1, Applicant submits that at least the operations of claim l directed to generating the modified, unbalanced data set also cannot be practically performed in the human mind, similarly to limitations in Examples 38 and 39. Applicant submits that any interpretation of the pending claims as including features that could reasonably be performed by the human mind is based on an unreasonably broad interpretation of the claims and is limited to consideration of only select portions of the claim language without consideration of the specification or understanding of a person of ordinary skill in the art.
It is respectfully submitted that this is not persuasive. Regarding Applicant’s first point, as set forth in MPEP 2106.04(II), Step 2A is a two-prong inquiry, in which examiners determine in Prong One whether a claim recites a judicial exception. MPEP 2106.04(I) sets forth that when determining whether a claim recites a judicial exception, it is sufficient to identify the claimed concept which aligns with at least one judicial exception, or, in other words, the specific claim limitations that the examiner believes may recite an exception. That the claim recites limitations which are in addition to those which recite judicial exceptions (i.e., additional elements) does not alter the analysis to determine whether a claim recites a judicial exception performed at Step 2A, Prong 1 (see MPEP 2106.04(II)(A)(1)). Those additional elements are examined at Step 2A, Prong 2, to determine whether the claim is directed to the judicial exceptions (see MPEP 2106.04(II)(A)(2)). As set forth in the above rejection, those limitations which are considered to recite a judicial exception are identified at Step 2A, Prong 1, and why they are considered to recite a judicial exception is explained, as is required by the eligibility analysis as outlined in MPEP 2106.04. It is noted that Applicant’s discussion of the recited additional elements as providing the data required for the performance of the judicial exceptions is in agreement with the analysis set forth in the above rejection.
Regarding Applicant’s second assertion that the generation of the modified data set does not recite mathematical concepts, it is noted that, in the above rejection, those steps are not considered to recite mathematical concepts but rather mental processes. However, other steps in the claim, such as “determining… that the candidate substitution produces a statistically significant effect on values” does recite a mathematical concept, as statistics is a mathematical analysis of data. Applicant has not submitted comments regarding this limitation specifically. Regarding Examples 38-39, it is noted that the claims are not analogous with those examples because the instant claims do not recite methods for applying transformations to digital facial images or generating random numbers.
Regarding Applicant’s third assertion that the claims do not recite mental processes, such arguments are not persuasive because Applicant has provided no reasoning that the indicated limitations could not be performed in the human mind or with the aid of pen and paper or computer. The claims require only creating a data set including experimental values and sequences of a number of proteins and manipulating and comparing values therein. This number encompasses anywhere from 2 to any reasonable number of proteins and their associated data, which could reasonably be processed mentally. Each of the claimed actions is also considered able to be performed mentally, as discussed in the above rejection. The indicated limitations of the claims do not recite actions which a human mind is incapable of performing, such as those recited in Examples 38-39 as pointed to by Applicant. Those examples, however, are not analogous to the instant claims as discussed above.
Ultimately, it is found that the claims recite additional elements which only serve a data gathering function or apply the judicial exception on a generic computer. Neither of these functions provide for a practical application at Step 2A, Prong 2, or provide significantly more at Step 2B.
Claim Rejections - 35 USC § 103
The outstanding rejections from the previous Office Action are withdrawn in view of the amendments submitted herein. Specifically, the closest prior art to Edelman et al. (WO 2002/054,063; previously cited) does not teach the limitation “based on the determination that the portion of the first differences is minimized with respect to the second differences for the subset of groupings, generating… a modified data set that (i) represents individual groupings of the subset of groupings as a single protein having a first normalized value of the Gibbs free energy change and a second normalized value of the unfolding temperature based on the values of the Gibbs free energy change and the values of the unfolding temperatures of the respective proteins included in the individual groupings and (ii) indicates associations between individual second proteins of the second group of the number of proteins and one or more single proteins corresponding to one or more individual groupings” recited in claims 1, 10, and 21, as argued by Applicant at p. 21-23.
Conclusion
No claims are allowed.
The claims appear to be free of the prior art. Neither the closest prior art to Edelman et al. (WO 2002/054,063; previously cited) or any references identified through the searches indicated on the search reports submitted herein do not teach, either alone or in combination, the limitation “based on the determination that the portion of the first differences is minimized with respect to the second differences for the subset of groupings, generating… a modified data set that (i) represents individual groupings of the subset of groupings as a single protein having a first normalized value of the Gibbs free energy change and a second normalized value of the unfolding temperature based on the values of the Gibbs free energy change and the values of the unfolding temperatures of the respective proteins included in the individual groupings and (ii) indicates associations between individual second proteins of the second group of the number of proteins and one or more single proteins corresponding to one or more individual groupings” recited in claims 1, 10, and 21.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
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 on (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 an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685