DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The IDS filed 9/13/2022 has been considered by the Examiner.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 63/025135 filed 5/14/2020 is acknowledged.
Status of Claims
Amendments to the claims filed 6/17/2026 are acknowledged.
Claims 1, 2, 5-20, and 22-34 are under examination.
Claims 3, 4, and 21 are cancelled.
Claim Rejections - 35 USC § 101
The instant rejection is maintained and modified in view of Applicant’s amendments filed 6/17/2026.
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, 5-20, and 22-34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1, 2, 5-20, and 22-30 are drawn to a method, so a process.
Claims 31-32 are drawn to non-transitory computer readable media, so a manufacture.
Claims 33-34 are drawn to a computer system comprising a process, so a machine.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
1. Accessing a molecule database and obtaining a target molecule.
This step reads on a mental process of considering a table or list of target molecules. The step is therefore an abstract idea.
2. Slicing the target molecule into molecular fragments, wherein the slicing comprises decomposing the target molecule using a retro-synthetic related decomposing function to obtain synthesizable fragments, wherein the retro-synthetic related decomposing function produces valid drug-like structures and is invertible so that obtained synthesizable fragments can be converted back to the target molecule.
This steps reds on a process that can be performed by the human mind because the “retro-synthetic related decomposing function” reads on a model or set of rules by which a molecule can be decomposed or regimented. Separating the bond and atom representations of a molecule to produce valid segments that are “valid” and “drug” like can be performed by the human mind or with the aid or paper pen. This step is therefore an abstract idea. Also see Step 2B.
3. Determining a fragment frequency of a plurality of molecular fragments of the target molecule.
The instant step reads on a decision making process that can be performed by the human mind and is therefore an abstract idea.
4. Calculating molecular descriptors for the molecular fragments.
The instant step reads on a mental process of calculating or math and is therefore an abstract idea.
5. Computing a fragment density for the target molecule as a number of atoms in the target molecule divided by a number of synthesizable fragments in the target molecule.
This step reads on a process that can be performed by the human mind because counting the number of atoms in a target molecule and dividing by synthesizable fragments can be performed mentally and with math. The step is therefore an abstract idea.
6. Calculating a synthetic difficulty score for the target molecule as a product between the fragment density and a sum of fragment scores weighted by the fragment frequencies.
The instant step reads on a mental process of calculating or math and is therefore an abstract idea. Calculating a product between a value for density and a value representing a sum is math and can also be achieved by the human mind.
Claim 15 is drawn to:
1. Selecting a target molecule.
The instant step reads on a mental process of selecting and is therefore an abstract idea.
2. Decomposing the target molecule into molecular fragments using a retro-synthetic related decomposing function selected from BRICS or RECAP algorithms, wherein the retro-synthetic related decomposing function produces synthesizable fragments that are valid molecular structures.
This step reads on a process of separating the molecular components by an algorithmic process used in BRICS or RECAP. The rules employed by BRICS or RECAP can be followed by the human mind and are therefore an abstract idea. Also see Step 2B.
3. Calculating a synthetic difficulty score for the molecular fragments for the target molecule.
The instant step reads on a mental process of calculating or math and is therefore an abstract idea.
4. Determining a sum of synthetic difficulty scores for the molecular fragments.
The instant step reads on a mental process of summing numerical values or math and is therefore an abstract idea
5. Determining a fragment density of the molecular fragments as a number of atoms in the target molecule divided by a number of molecular fragments in the target molecule.
The instant step reads on a step that can be performed by the human mind using math and is therefore an abstract idea.
6. Calculating the synthetic accessibility score as a product between the fragment density and the sum of the synthetic difficulty score weighted by fragment frequencies.
The instant step reads on a step that can be performed by the human mind using math and is therefore an abstract idea.
7. Proving the synthetic accessibility score for the target molecule.
The instant step reads on a mental process of thinking to determine a score and is therefore an abstract idea
Claims 1, 2, 5-15, 16-20, and 22-34 further recite steps that read on mental processes and math and are therefore also abstract ideas.
Step 2A Prong Two: Consideration of Practical Application
The claimed process results in a step of calculating and storing a difficulty score (claim 1) and calculating and providing a synthetic accessibility score (claim 15), which are abstract idea steps with extra solution activity of storing or outputting. See MPEP 2106.05(g). The claims do not recite any additional elements that integrate the abstract idea into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
1. Storing the synthetic difficulty score in a database having a plurality of synthetic difficulty scores for a plurality of molecules, as in claim 1.
2. providing the synthetic accessibility score, as in claim 15.
3. Using BRICS or RECAP software.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because storing a determined result and providing a numerical value which reads on outputting are both tangential extra solution activities as described in MPEP 2106.05(g). The steps are well known, routine and conventional limitations that do not add significantly more to the recited abstract idea.
Furthermore, in an alternative embodiment to an abstract idea, BRICS and RECAP may be interpreted as an additional element or software package. However, BRICS and RECAP are well known algorithmic methods available as programs. Implementing BRICS or RECAP is well known, routine and conventional.
Other elements of the method include non-transitory computer readable medium (claims 31-32) and a processor (claims 33-34) which is a recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 6/17/2026 have been fully considered but they are not persuasive.
Applicants argue (Remarks, page 11, par. 2) that the claims have been amended to recite a retrosynthetic-related decomposing function (claim 1) and BRICS or RECAP (in claim 15). Applicants argue that function must meet specific technical criteria where “each fragment has to be useful with bijective mapping, such that it should be possible to compose a molecule back given its obtained fragments" and "any of the resulting fragments has to be an elementary building block, such that each fragment can be a part of a chemical reaction (reactants) to reach the target molecule," as disclosed in the specification at paragraph [055].
In response, under Broadest Reasonable Interpretation (BRI), retrosynthetic-related decomposing function is interpreted as a model or set of rules for segmenting a molecule. The analysis required to segment a molecule such that its fragments can be composed back is a process that can be performed by the human mind. With respect to using BRICS or RECAP algorithms, the claim is not specific with respect to which BRICS or RECAP algorithms are used and to what extent. BRICS or RECAP are well known, routine algorithms in computer program form. Therefore even if interpreted as an additional element under Step 2B, using BRICS or RECAP to segment a molecule is considered well know, routine and conventional or a well known step of data collection as described in MPEP 2106.05(g).
Applicants argue (Remarks, page 11, par. 3) that the decomposition using retrosynthetic-related algorithms such as BRICS or RECAP cannot practically be performed by the human mind.
In response, Applicant’s argument is an assertion without an explanation of why the algorithm used in BRICS or RECAP can not be performed as a mental process and/or with math. The implementation of a computer or computer environment (i.e. a program) to process steps that can be executed by the mind or with math is not sufficient to render claims statutory.
Applicants argue (Remarks, page 12, par. 1) the steps of “computing a fragment density” and “calculating a synthetic difficulty score.” Applicants point to the specification (par. 073) disclosing that fragment density increases with increasing number of atoms and decreases with increasing number of fragments. Applicants argue that the limitations are specific computational operations.
In response, specificity per se is not a criterial in the Two Step analysis in 35 USC 101. The pointed to limitations, while having a specific calculational outcome, are steps that can be performed by the human mind and/or with math. Therefore, even while being specific, a step drawn to a mental analysis or math remains an abstract idea.
Applicants argue (Remarks, page 12, par. 2) argue that the claims recite a practical application under Step 2A Pron Two. Applicants argue that the claimed process provides a specific technical improvement in the field of computational chemistry and drug discovery.
In response, the claims currently do not recite any “additional elements” that would integrate the recited abstract idea into a practical application. Applicants are advised to review the specification for physical world embodiments that could constitute a “practical application.” Categories of “practical application” are listed above under Step 2A Prong Two.
Applicants argue that under Step 2B the claims recite additional elements that amount to significantly more. Applicants point to a specific use of “a retrosynthetic-related decomposing function” that “produces valid drug-like molecular structures,” and the use of BRICS or RECAP algorithms.
In response, a generically recited “retrosynthetic-related decomposing function” reads on a set of rules or mathematics that can be performed by the human mind to segment a molecule, and therefore reads on an abstract idea. The algorithms used by BRICS or RECAP also read on steps that can be performed by the human mind. Alternatively, even should BRICS or RECAP are to be considered as an “additional element,” these would not be sufficient under Step 2B to render the claim statutory because BRICS or RECAP are routine, conventional and well understood.
For the reasons set forth above, the 35 USC 101 rejection is maintained.
Claim Rejections - 35 USC § 112-2nd paragraph
The rejection of claims 18-19 and 29 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of Applicant’s amendments filed 6/17/2026.
Claim Rejections - 35 USC § 103
The rejection of claims 1-34 under 35 U.S.C. 103(a) as being unpatentable over Ertl et al. (Journal of Cheminformatics, vol. 1 (2009) pgs 1-11; 8/13/2022) is withdrawn in view of Applicant’s amendments.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373. The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-7035. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anna Skibinsky/
Primary Examiner, AU 1635
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