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 .
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 September 19, 2025 has been entered.
Status of the Claims
Claims 3, 5-11, 13, and 15-24 are under examination.
Claim Rejections - 35 USC § 101
3. 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 3, 5-11, 13, and 15-24 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more.
Claims 3, 5-11, 13, and 15-24 are directed to method of determining the average electron density of a molecule or designing a molecule having a desired material, chemical or pharmaceutical properties. As described in Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S._, 134 S. Cr. 2347, 110 U.S.P.Q.2d 1976 (2014), a two-step analysis is required in considering the patent eligibility of the claimed subject matter. The first step requires determining if the claimed subject matter is directed to a judicial exception. The instant claims require the steps of generating a list of molecules; generating a table of atoms wherein each atom is identified by a combination of each atom’s specific elemental type and environment wherein the identification includes selecting all non-covalently bounded second degree neighboring atoms within 1.5 to 5 Angstroms from each first degree neighboring atom of each molecule; generating average electron densities for each part of the molecules using a AED tool; selecting a molecule; identifying the further molecule’s environment wherein said identifying include selecting all non-covalently bounded second degree neighboring atoms within 1.5 to 5 Angstroms from each first degree neighboring atom; finding an environment from the table of atoms; predicting the average electron density of the further molecule; matching the average electron density of the atoms of the further molecule to an average electron density of atoms in a target molecule, selecting the identified matching further molecules for further analysis, constructing a molecular model of the identified matching further molecule, binding the molecular model to an active site of a receptor, filtering and screening the identified matching further molecules having the desired material, chemical, or pharmaceutical properties, designing the screened identified matching further molecules, wherein the designed matching further molecules are used for one or more activities. The steps of generating a list of molecules, generating a table of atoms, selecting a further molecule, identifying a further molecule’s environment, selecting all non-covalently bounded second degree neighboring atoms, finding an environment and selecting the identified matching further molecule are mental steps. Mental steps are a judicial exception. The steps of generating average electron densities for each part of the molecules using a AED tool, predicting the average electron density of the further molecule; matching the average electron density of the atoms of the further molecule to an average electron density of atoms in a target molecule, constructing a molecular model of the identified matching further molecule, binding the molecular model to an active site of a receptor, filtering and screening the identified matching further molecules having the desired material, chemical, or pharmaceutical properties, designing the screened identified matching further molecules, wherein the designed matching further molecules are used for one or more activities are drawn to mathematical algorithm as shown in the specification on pages 18 and 19. Dependent claims 5-11, 13, 15, 16, and 18-24 recite additional mathematical steps for the algorithm or the data for the mathematical algorithm. The courts have found mathematical algorithms to be drawn to the judicial exception of an abstract idea (In re Grams, 888 F.2d 835, 12 U.S.P.Q.2d 1824 (Fed. Cir. 1989)). Thus, the instant claims are drawn to a judicial exception.
This judicial exception is not integrated into a practical application. The instant claims do not recite an element that reflects an improvement in the functioning of a computer or other technology, an element that applies the judicial exception to effect a particular treatment, an element that implements the judicial exception with a particular machine, or an element that effects a transformation of a particular article to a different state or thing.
The second part of the analysis requires determining if the claims include additional elements that are sufficient to amount to significantly more than the judicial exception. The instant claims do not recite an additional element to the judicial exception. In addition, the recitation of the specific types of data to be used in the judicial exception does not transform the abstract idea into a non-abstract idea. (See buySAFE, Inc. v Google, Inc. 765 F.3d 1350, 112 U.S.P.Q.2d 1093 (Fed.Cir.2014)).. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Response to Arguments
4. Applicant state that measuring non-covalently bounded second degree neighboring atoms within 1.5 to 5 Angstroms is not extra solution activity. Applicant has removed this limitation, and the argument is moot. It is noted that the amendment of selecting non-covalently bounded second degree neighboring atoms within 1.5 to 5 Angstroms is a mental step, as one of ordinary skill in the art could identify and choose these atoms given a dataset that shows the distance between atoms. As a mental step and part of the judicial exception, this step does not provide a practical application or an additional element that is significantly more than the judicial exception.
Applicant states that “the presently pending claims are directed to an entirely new method based on using these existing algorithms (which cannot be mentally solved) to build a table of reference values.” (page 22) Applicants state that the claimed invention is a “quick and accurate method for creating and analyzing a molecule having desired chemical, material, or pharmaceutical properties” (page 23). However, the claimed method of analyzing molecules is drawn to a judicial exception for the reasons given above. As a whole, the instant claims are drawn to mental steps and mathematical steps for the reasons provided above. As a whole, the instant claims do not integrate the judicial exception into a particular machine, a particular transformation, or a particular treatment. The instant claims do not recite any additional element to the judicial exception that is not well understood, conventional or routine.
Applicant states that the mere presence of an algorithm in addition to concrete steps does not make the entire claim abstract and cites Thales Visionix Inc. v. United States for support. However, the instant claims may be distinguished from Thales. In Thales, the claimed invention related the positioning and use of inertial sensors. In contrast, the instant claims are drawn solely to data processing and mathematical modeling.
Applicant state that the instant claims are drawn to an improvement in CADD, and that CADD is patentable subject matter. The Examiner did not suggest that the field of CADD is not patent eligible. The Examiner did not suggest that particular classes and subclasses of subject matter are not patent eligible. The office action is directed only this application and the particular facts of this application. In this instance, for the reasons given above, the claimed invention is not patent eligible. If applicants are stating that the claimed invention offer an improvement in analyzing a molecule having desired chemical, material, or pharmaceutical properties, the improvement in this analysis is an improvement in the judicial exception. An improvement in a judicial exception is not an improvement in a technology.
Applicant states that matching the average electron density of the atoms, constructing a model, binding a molecular model, filtering and screening, and designing the screened identified molecule are not drawn to mathematical algorithms. However, matching the average electron density is a mathematical process as it is matching numerical values. The instant claims require that the average electron density value is within 10% deviation from the average electron density of the atoms of the target molecule. Determining the percent deviation is a mathematical process. In addition, Instant claims 15 and 16 show that the matched values need to be within 3% or 1% deviation, which supports that matching average electron densities is a mathematical process.
Furthermore, the prior art teaches that constructing a molecular model is a mathematical algorithm. Terwilliger (“SOLVE and RESOLVE: Automated Structure Solution, Density Modification, and Model Building”, J. Synchrotron Rad. (2004), Number 11, pages 49-52) teaches using a mathematical algorithm for matching numerical values matching electron densities (page 50, right column) as well as using Fast Fourier Transform (FFT) procedure for constructing a molecular model (page 51, right column). A FFT procedure is a mathematical algorithm.
It is also known in the art to use mathematical algorithms to identify binding to a molecular model, filtering and screening those models according to a criteria, and designing a molecule. Novikov et al. (“Improving Performance of Docking-Based Virtual Screening by Structural Filtration” J. Mol. Model (2010) 16:1223-1230) teaches using ligand docking and binding energy calculations to determine if a molecular model binds to a receptor of interest (page 1224, right column). Novikov et al. also teach filtering and screening using a mathematical process (pages 1224, right column-page 1226, left column) as well as designing a molecule (pages 1229, right column to pages 1230, left column).
Both Terwilliger and Novikov et al. show that matching electron densities, constructing a molecular model, binding the molecular model, filtering and screening the molecular models, and designing a molecule are drawn to mathematical algorithms. Thus, the instant claims are drawn to mathematical algorithms and mental steps for the reasons provided above.
Applicant states the claimed invention has the application of constructing, creating, screening and designing candidate molecules. To determine a practical application, the instant claims need to demonstrate a particular treatment, particular machine, particular physical transformation, or an improvement in a technology. The steps of constructing, creating, screening, and designing candidate molecules are limited to molecular models. Furthermore, these steps are drawn to a judicial exception. Thus, the instant claims do not offer a particular treatment, particular machine, particular physical transformation, or an improvement in a technology. Thus, the instant claims do not integrate the judicial exception into a practical application.
Applicant states that the Examiner agrees with the that the instant claims recite synthesizing these pharmaceuticals or treatments in patients. The Examiner made a typographical error in the previous office action. The instant claims clearly do not recite synthesizing pharmaceutical or treatments in patients. Since the instant claims do not recite synthesizing pharmaceutical or treatments, the instant claims do not result in improved pharmaceutical drugs or treatments.
Applicant states that there is no requirement that the molecules be synthesized to qualify a real-world application. Applicant states that there are many patented inventions in CADD, molecular modeling, and bioinformatics that involve in silico predictions, simulations, and computational screening. As stated above, this office action is directed to the instant applications and the particular facts of this application. The Examiner is not attempting to examine entire fields of subject matter. In this instance, the instant claims do not integrate the judicial exception into a practical application or provide an element that is significantly more that the judicial exception.
Applicant states that the instant claims use the computational method for “predicting an average electron density of the one or more further molecules or for a part of the one or more further molecules based on the matching environment from the table of atoms from each atom in the one or more further molecules” to identify molecules that are more or less likely to cure a condition. Applicants state that this is a real-world practical use in drug discovery. In order to determine if there is a practical application to the judicial exception, the instant claims must include an element that reflects an improvement in the functioning of a computer or other technology, an element that applies the judicial exception to effect a particular treatment, an element that implements the judicial exception with a particular machine, or an element that effects a transformation of a particular article to a different state or thing. In this instance, the predicting step, as described as matching environment from the table, is drawn to a mathematical algorithm. Alternatively, matching an environment for the table may be interpreted as a mental step, since one of ordinary skill in the art is capable to comparing values and determining their similarities. As mathematical algorithm or a mental steps, this limitation recites a judicial exception and does not recite an improvement in a technology, a particular treatment, particular machine, or a transformation of a particular article to a different state or thing.
Applicants state that the combination of the method steps results in improved computer-aided design achieved with increased rapidity and enhanced accuracy. As stated the above, the claimed method of analyzing molecules is drawn to a judicial exception. As a whole, the instant claims are drawn to mental steps and mathematical steps for the reasons provided above. The improvement provided by the instant claims would be an improvement in the analysis of molecules. However, the improvement of the analysis is an improvement of a judicial exception and not an improvement of a technology.
Applicant states that the claimed invention is easier to use and results in significant cost savings. However, saving time, money, computer resources, CO2 emission by obtaining quick accurate predictions of AEDs and to obtain new hit compounds are improvements that are the result of the improvement to the mathematical algorithm or judicial exception. An improvement to the judicial exception is not an improvement in technology.
Applicant states that the claimed method step involves quantum simulations and transforms the outcome of the simulations to guidelines. The quantum simulations (as in claim 5) are drawn to a mathematical algorithm. While a mathematical algorithm may require the use of a computer, it remains a mathematical algorithm, which the courts have recognized to be a judicial exception. In addition, the MPEP §2106.05(c) states, “Another consideration when determining whether a claim integrates a judicial exception into a practical application in Step 2A Prong Two and whether a claim recites significantly more in Step 2B is whether the claim effects a transformation or reduction of a particular article to a different state or thing. . . .An ‘article’ includes a physical object or substance. The physical object or substance must be particular, meaning it can be specifically identified. “ In this instance, the transformation of the outcome of the simulations to guidelines is not transformation of a physical object or substance. Thus, the claims do not recite a particular transformation that integrates the judicial exception into a practical application.
Applicant states that claims 6-10 do not relate to any mathematical algorithm. However, as stated above, generating a table of atoms is a mental step. One of ordinary skill in the art could create such a table using the data of claims 6-9. Identifying the data to be put into the table does not transform the judicial exception into patent eligible subject matter. Applicant state that the step of binding a molecular model is not a mathematical algorithm. However, as shown above, determining the binding of a molecular model is performed using mathematical algorithm. Claim 10 merely describes the data to be used in that mathematical algorithm. The recitation of the specific types of data to be used in the judicial exception does not transform the abstract idea into a non-abstract idea
Applicant states that since the claimed invention is novel, the steps of the claimed invention are not well-understood, conventional or routine. While the claimed invention may be novel, the instant claims are drawn to a judicial exception. Whether the judicial exception is not well-understood, conventional or routine is not relevant to patent eligibility. The instant claims do not recite an element in addition to the judicial exception that is not well-understood, conventional or routine. Thus, the instant claims do not recite something significantly more than the judicial exception.
Applicant states that the claimed invention as created a “new tool” rather than classic “AED tools”. However, this “new tool” is drawn to a judicial exception for the reasons above. The description of a biologically and therapeutically threshold that is used in the judicial exception, does not transform the judicial exception into patent eligible subject matter. The threshold is data that is used in the analysis, but it does not change the analysis itself into different subject matter.
Applicant states that a very specific machine have a very specific set of instructions were necessary to obtain this percentage threshold. However, instant claims do not recite a particular machine. The Examiner cannot import limitations from sources outside the instant claims.
Applicant states that the claimed method as the practical application of discovering new molecules having desired activity. However, the instant claims do not recite an improvement in a technology, a particular machine, a particular physical transformation or a particular treatment. Thus, the instant claims do not integrate the judicial exception into a practical application.
Applicant states that constructing a molecule is not a mathematical algorithm. The Examiner has shown that constructing a molecular model is mathematical algorithm above. Furthermore, the MPEP §2106.05(c) states, “Another consideration when determining whether a claim integrates a judicial exception into a practical application in Step 2A Prong Two and whether a claim recites significantly more in Step 2B is whether the claim effects a transformation or reduction of a particular article to a different state or thing. . . .An ‘article’ includes a physical object or substance. The physical object or substance must be particular, meaning it can be specifically identified. “ In this instance, the transformation of the molecular model is not a transformation of a physical object or substance.
Applicant states that a computational tool is tied to a specific technological process, improves a technical field, or provides a technological solution should be considered patent-eligible. Applicant cites DDR Holding v Hotels.com, Enfish, LLC v. Microsoft Corp, and Vanda Pharmaceuticals v West-Ward for support. However, the instant application is distinguishable from all three cases. In DDR Holding v Hotels.com, the court found that the invention as issue was necessarily rooted in computer technology to overcome a problem specifically arising the realm of computer networks. In the instant case, the claims are not drawn to solving a problem that is necessarily rooted in computer technology. While the instant claims may use computers, the use of computer does not equate to a problem rooted in computer technology.
In Enfish, LLC v. Microsoft Corp., the claims were drawn to a table that rendered the claims in Enfish patent eligible, because the self-referential table in Enfish provided an improvement in the functioning of the computer itself. In the instant case, the claims do not improve the functioning of the computer itself. A computer is merely used to implement the judicial exception.
In Vanda Pharmaceuticals v West-Ward, the court found that the claimed invention require the doctor to administer iloperidone. The court found that administering iloperidone was an application of a natural relationship which provided a particular treatment. In the instant case, the claimed invention does not provide an improvement in a technology, a particular machine, a particular physical transformation or a particular treatment. Thus, the instant claims do not integrate the judicial exception into a practical application.
Applicant states that the claimed invention offers an improvement in the functioning of the computer or other technology. Applicant states that the claimed invention offers the practical technical solution of advancing molecular design in a timely and cost-effective manner. First, the claimed invention does not alter the functioning of a computer. Thus, the claimed invention cannot improve the functioning of a computer. Secondly, saving time and money are improvements that are the result of the improvement to the mathematical algorithm or judicial exception. An improvement to the judicial exception is not an improvement in technology.
Applicant state that the 10% threshold is non-trivial and lead to accurate predictions of further molecules having matching AED values. However, including the 10% threshold in a judicial exception does not transform that judicial exception. The claimed invention remains drawn to mathematical and mental steps. While the claimed invention may offer an improvement in prediction, this is an improvement in the judicial exception itself and not an improvement in a technology.
Applicant states that the claimed invention offers a transformation of previously inaccurate methods into the currently claimed accurate methods. Applicant states that a physical transformation is not required. The MPEP §2106.05(c) states, “Another consideration when determining whether a claim integrates a judicial exception into a practical application in Step 2A Prong Two and whether a claim recites significantly more in Step 2B is whether the claim effects a transformation or reduction of a particular article to a different state or thing. . . .An ‘article’ includes a physical object or substance. The physical object or substance must be particular, meaning it can be specifically identified. “ The instant claims to not recite a transformation of a physical object or substance.
Applicant states that it is the burden on the Examiner to show that the presently claimed methods will not function as intended. The Examiner has not made any statement regarding if the claimed method will or will not function. In the instant case, the claimed invention is drawn to mathematical and mental steps which are a judicial exception. The instant claims do not provide a practical application that integrates the judicial exception or something that is significantly more than the judicial exception. Physically creating the compound is one way of demonstrating a physical transformation that integrates the judicial exception into a practical application. The applicant is not limited to demonstrating a physical transformation to demonstrate that the claimed invention is patent eligible.
Applicant states that a table based approach has already been confirmed by the Federal Circuit as a basis for patentable subject matter. The applicants cite Enfish, LLC v. Microsoft Corp. However, it was not because the claims were drawn to a table that rendered the claims in Enfish patent eligible, but it was because the self-referential table in Enfish provided an improvement in the functioning of the computer itself. In the instant case, the claims do not improve the functioning of the computer itself. The computer is merely used to implement the judicial exception. Furthermore, improving the process of identifying compounds with desired properties by making it more accurate a systematic than prior conventional methods is an improvement in the judicial exception itself. An improvement in the judicial exception itself is not an improvement in a technology.
Applicant cites McRO, Inc v Bandai Namco Games to support using specific rules to achieve improved results are not abstract. The instant case is distinguishable from the McRO, Inc v Bandai Namco Games. In McRO, Inc v Bandai Namco Games, the claims at issue resulted in animated characters to produce lip synchronization and facial expression control of the animated characters. Unlike the animated characters in McRO, Inc v Bandai Namco Games, the result of the instant claims is a data resulting from an improvement of a judicial exception. An improvement in the judicial exception itself is not an improvement in a technology.
Applicant cites SiRF Technology, Inc. v International Trade Commission for support. The instant case is distinguishable from SiRF Technology, Inc. v International Trade Commission. In SiRF Technology, Inc. v International Trade Commission, the claims at issue required a GPS receiver. The GPS receiver proved a particular machine that integrates the judicial exception into a practical application. The instant case does not recite a particular machine and does not integrate the judicial exception into s practical application.
Applicant cites Research Corp. Technologies, Inc. v. Microsoft Corp to support that the manipulations of computer data structures and the output of modified computer data structure was patentable subject matter. The court in Research Corp. Technologies, Inc. v. Microsoft Corp does not mention data structures. Rather, the claims at issue were drawn to a method of halftoning gray scale images by utilizing pixel by pixel comparison of the image against a blue noise mask. The court found that the claims at issue were rooted in computer technology, and were patent eligible. The instant claims are not rooted in computer technology.
Applicants states the claimed method use of a computer supports the patentability of the instant claims. However, the instant claims contain no recitation of a computer. The instant claims do not recite any structural limitations of a computer or what is programmed on the computer. The Examiner cannot import limitations into the claims. Thus, the instant claims do not recite a particular machine.
Applicant states that binding molecules is not about using a mathematical algorithm. First it is noted that manipulating molecular geometry is a mathematical process. Secondly, Novikov et al. (“Improving Performance of Docking-Based Virtual Screening by Structural Filtration” J. Mol. Model (20100 16:1223-1230) teaches using ligand docking and binding energy calculations to determine if a molecular model binds to a receptor of interest (page 1224, right column). Binding molecules in a molecular model is drawn to a mathematical algorithm.
Applicant states that the instant claims provides the specific transformation of individual atoms into the desired molecules of interest. However, this transformation is not a physical transformation and does not integrate the judicial exception into a practical application.
Applicants states that the “AED tool” is significantly more than the judicial exception. However, as stated above, the AED tool itself is a judicial exception. Since the AED tool is a judicial exception, it does not provide an additional element to the judicial exception that is significantly more than the judicial exception.
This rejection is maintained and modified as necessitated by amendment.
Withdrawn Rejections
5. Applicant’s arguments and amendments, filed July 9, 2025, with respect to the rejection made under 35 U.S.C. §112 have been fully considered and are persuasive. The amendments are sufficient to overcome the rejection. This rejection has been withdrawn.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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/JERRY LIN/Primary Examiner, Art Unit 1685