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 .
Claim Status
Claims 1-18 are pending and examined herein.
Claims 1-18 are rejected.
Priority
Claims 1-18 are granted the claim to the benefit of priority to U.S. Provisional application 61/883919 filed 27 September 2013. Thus, the effective filling date of claims 1-18 is 27 September 2013.
Information Disclosure Statement
The information disclosure statement (IDS) was received on 03 January 2023. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Drawings
The drawings received 12 April 2022 are objected to for containing colored figures. Figures 1B and 1C are objected to for being colored figures. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 820 and 822 in figure 4. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on page 77 in line 21. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 101
The claims are patent eligible under 35 USC 101 for the reason stated below.
The claims recite judicial exceptions that are abstract ideas (i.e. mental processes and mathematical concepts) such as filtering the unfiltered data set, training a plurality of sequence activity models, testing the plurality of sequence activity models predictive abilities, identifying, as the filtered data subset, a data subset that is used to train a sequence activity model having a higher predictive ability, applying a sequence activity model trained using the filtered data subset, and identifying one or more new variant biomolecules that are predicted by the sequence activity model in independent claim 1. Although the claims recite judicial exceptions, the claims are patent eligible because the additional element of “synthesizing or expressing the one or more new variant biomolecules identified in (c), wherein the one or more new variant biomolecules’ activities on the ligand are improved over the plurality of variant biomolecules as measured by an assay” integrates the judicial exceptions into a practical application by providing an improvement to the biomolecules that are synthesized or expressed by providing biomolecules that have improved activities on the ligand. Since the improvement is realized in the additional element of synthesizing or expressing the improved biomolecule, the claims as a whole provide an improvement to technology.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,342,046. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are anticipated by claims 1-18 of U.S. Patent No. 11,342,046.
Claim 1 is directed to (a) receiving, by the computer system, an unfiltered data set comprising the following information for each of a plurality of variant biomolecules: (i) the variant biomolecule's activity on a ligand in a binding site of the variant biomolecule, (ii) a sequence of the variant biomolecule, wherein the sequence is a nucleic acid sequence or a protein sequence, and (iii) one or more geometric parameters characterizing the geometry of the variant biomolecule regarding the ligand in the binding site of the variant biomolecule
The patent shows receiving an unfiltered dataset having information for each of a plurality of variant biomolecules of the variant biomolecules activity on a ligand in a binding site of the variant biomolecule, a sequence of the variant biomolecule, wherein the sequence is a nucleic acid or protein, and one or more geometric parameters characterizing the geometry of the variant biomolecule regarding the ligand in the binding site of the variant biomolecule (patent claim 1 lines 4-10).
(b) filtering, by the one or more processors, the unfiltered data set to generate a filtered data subset, comprising: obtaining a plurality of data subsets from the unfiltered data set, each data subset is obtained by removing from the unfiltered data set at least one of the geometric parameters of the plurality of variant biomolecules and/or removing certain variant biomolecules having geometric parameter values outside defined ranges
The patent shows filtering the unfiltered data set to generate a filtered data subset comprising obtaining a plurality of data subsets by removing from the unfiltered data set at least one of the geometric parameters of the plurality of variant biomolecules and/or removing certain variant biomolecules having geometric parameter values outside defined ranges (patent claim 1 lines 11-17).
training a plurality of sequence activity models, wherein each of the plurality of sequence activity models is trained using a data subset of the plurality of data subsets, and wherein the sequence of the variant biomolecule and one or more of the geometric parameters are independent variables of the sequence activity models and the variant biomolecule's activity on the ligand is a dependent variable of the sequence activity models
The patent shows training a plurality of sequence activity models using a subset of the plurality of data subsets, wherein the sequence and the geometric parameters are independent variables of the sequence activity models and the variant biomolecules activity on the ligand is a dependent variable of the model (patent claim 1 lines 18-22).
testing the plurality of sequence activity models' predictive abilities to predict variant biomolecules' activities on the ligand,
The patent shows testing the plurality of sequence activities models’ predictive abilities to predict variant biomolecules’ activities on the ligand (patent claim 1 lines 23-24).
and identifying, as the filtered data subset, a data subset that is used to train a sequence activity model having a higher predictive ability than a sequence activity model trained with the unfiltered data set;
The patent shows identifying as the filtered data subset a date subset that is used to train a sequence activity model having a higher predictive ability than a sequence activity model trained with the unfiltered data set (patent claim 1 lines 25-27).
(c) applying, by the one or more processors, a sequence activity model trained using the filtered data subset to a plurality of new variant biomolecules, and identifying, using the one or more processors, one or more new variant biomolecules that are predicted by the sequence activity model trained using the filtered data subset to have a desired level of the activity on the ligand, wherein each variant biomolecule of the plurality of new variant biomolecules is different from the plurality of variant biomolecules;
The patent shows applying a sequence activity model trained using the filtered data subset to a plurality of new variant biomolecules, and identifying one or more new variant biomolecules that are predicted but the sequence activity model trained using the filtered data subset as having a desired level of activity, wherein each variant biomolecule for the plurality of new variant biomolecules is different from the plurality of variant biomolecules (patent claim 1 lines 28-33).
and (d) synthesizing or expressing the one or more new variant biomolecules identified in (c), wherein the one or more new variant biomolecules' activities on the ligand are improved over the plurality of variant biomolecules as measured by an assay.
The patent shows synthesizing or expressing the one or more new variant biomolecules identified in (c) and assaying the one or more new variant biomolecules’ activities on the ligand, wherein the one or more new variant biomolecules’ activities on the ligand are improved over the plurality of variant biomolecules (patent claim 1 lines 34-38). This shows the assay is used to show the one or more new variant biomolecules’ activities on the ligand are improved.
Regarding instant claims 2-18, Patent 11,342,046 shows the same claimed subject matter in claims 2-18 of the patent and anticipates instant claims 2-18.
Conclusion
No claims are allowed.
The closest prior art is Gustafsson et al. (US 20060136184 A1; cited in IDS received 03 January 2023) which shows designing and synthesizing sequences that possess desired properties, utilizing a sequence-activity model to calculate properties of variant biomolecules using the variant sequences that have been trained to map sequences to its activity, applying these models to identify new variant biomolecules, synthesizing or expressing variant sequences, and assay these synthesized variant sequences to measure experimental values. However, Gustafsson et al. does not show using one or more geometric parameters characterizing the geometry of the variant biomolecule regarding the ligand in the binding site of the variant biomolecule or the particular method of filtering the unfiltered data subset by removing at least one of the geometric parameters and/or removing certain variant biomolecules having geometric parameter values outside a defined range.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at 571-272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/J.E.H./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685