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 .
Election/Restrictions
Applicant’s election of group I, pertaining to claims 1-16, and election of species a, pertaining to claim 8, in the reply filed on 01/16/2026 is acknowledged.
Claims 9, 10, 14, 15, 17, and 18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention(s), there being no allowable generic or linking claim.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims Status
Claims 1-18 are pending.
Claims 9, 10, 14, 15, 17, and 18 are withdrawn.
Claims 1-8, 11-13, and 16 are examined.
Priority
The instant application claims priority to US Provisional Application No. 63/175767, filed 04/16/2021, and US Provisional Application 63/175495, filed 04/15/2021. Therefore, the Effective Filing Date (EFD) assigned to each of the claims 1-8, 11-13, and 16 is the provisional filing date of Application 63/175495, filed 04/15/2021.
Information Disclosure Statement
The Information Disclosure Statements filed 08/24/2022, 03/02/2023, 09/14/2023, 08/29/2024, 04/03/2025, and 07/22/2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Drawings
The drawings filed 03/24/2022 are objected to as failing to comply with 37 CFR 1.84(p)(4) because reference characters "2104" and "2004" have both been used to designate “Distance Channels”. Furthermore, reference character “2004” has been used to designate both “Distance Channels” and “Annotation Channel”.
Furthermore, the drawings are objected to because in Figure 7, “Distance Channel Temnsor” should read “Distance Channel Tensor”.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) 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. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. 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.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-8, 11-13, and 16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
With respect to claim 1, the claim recites the limitation of “wherein the nearest cell is selected based on matching element coordinates”. The claim is indefinite because it is unclear if this is an active step that must be performed within the confines of the claim or rather if the selecting based on matching element coordinates is an intended use of the method.
With further respect to claim 1, the claim recites the limitation of “wherein the neighborhood cells are […] selected based on being within a distance proximity”. The claim is indefinite because it is unclear if this is an active step that must be performed within the confines of the claim or rather if selecting of neighborhood cells is an intended use of the method.
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 1-8, 11-13, and 16 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims are directed to a method.
With respect to step (2A)(1): The claims are directed to abstract ideas of mathematical concepts and mental processes.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mathematical concepts recited in claim 1:
generating an element-to-cells mapping that maps, to each of the elements, a subset of the cells
wherein the subset of the cells mapped to a particular element in the sequence includes a nearest cell in the grid and one or more neighborhood cells in the grid
wherein the neighborhood cells are contiguously adjacent to the nearest cell and selected based on being within a distance proximity range from the particular element
generating a cell-to-elements mapping that maps, to each of the cells, a subset of the elements
wherein the subset of the elements mapped to a particular cell in the grid includes those elements in the sequence that are mapped to the particular cell by the element-to-cells mapping
Mental processes recited in claim 1:
wherein the nearest cell is selected based on matching element coordinates of the particular element to the cell coordinates
using the cell-to-elements mapping to determine, for each of the cells, a nearest element in the sequence
wherein the nearest element to the particular cell is determined based on distances between the particular cell and the elements in the subset of the elements
Dependent claims 2-8, 11-13, and 16 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 2: “wherein the matching the element coordinates of the particular element to the cell coordinates further includes truncating a decimal portion of the element coordinates to generate truncated element coordinates”
Claim 3: “for a first dimension, matching a first truncated element coordinate in the truncated element coordinates to a first cell coordinate of a first cell in the grid, and selecting a first dimension index of the first cell”, “for a second dimension, matching a second truncated element coordinate in the truncated element coordinates to a second cell coordinate of a second cell in the grid, and selecting a second dimension index of the second cell”, “for a third dimension, matching a third truncated element coordinate in the truncated element coordinates to a third cell coordinate of a third cell in the grid, and selecting a third dimension index of the third cell”, “using the selected first, second, and third dimension indices to generate an accumulated sum based on position-wise weighting the selected first, second, and third dimension indices by powers of a radix”, “using the accumulated sum as a cell index for selection of the nearest cell”
Claim 4: “wherein the distances are calculated between cell coordinates of the particular cell and element coordinates of the elements in the subset of the elements”
Claim 5: “wherein the sequence is a protein sequence of amino acids”
Claim 6: “wherein the elements are atoms of the amino acids”
Claim 7: “wherein the steps of generating the element-to-cells mapping, generating the cell-to-elements mapping, and using the cell-to-elements mapping to determine, for each of the cells, the nearest element have a runtime complexity of O(a * f+ v), wherein a is a number of the atoms, f is a number of the amino acids, v is a number of the cells, and * is a multiplication operation”
Claim 8: “wherein the atoms include alpha carbon atoms”
Claim 11: “wherein the cells are three-dimensional voxels”
Claim 12: “wherein the cell coordinates are three-dimensional coordinates”
Claim 13: “wherein the element coordinates are three-dimensional coordinates”
Claim 16: “wherein the sequence includes M elements, wherein the subset of the elements includes N elements, and wherein M>>N”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than using mathematical concepts to and mental processes to encode amino acid sequences and analyze the sequences.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is 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 exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claim 1 recites the following additional elements that are not abstract ideas:
computer-implemented
The additional element is interpreted as mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea 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 (see MPEP 2106.05(f)).
None of the dependent claims recite additional elements and thus none of the dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2016.05(d).I, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either 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 claim 1: The additional element of a computer-implemented method does not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes 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 abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-8, 11-13, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Torng et al. (“3D deep convolutional neural networks for amino acid environment similarity analysis”, BMC Bioinformatics, 2017).
Regarding claim 1, Torng et al. teaches a method comprising:
generating an element-to cells mapping that maps, to each of the elements, a subset of the cells, wherein the subset of the cells mapped to a particular element in the sequence includes a nearest cell in the grid and one or more neighborhood cells in the grid (page 4, column 1).
wherein the nearest cell is selected based on matching element coordinates of the particular element to the cell coordinates (Figure 5 description; page 14, column 1, paragraph 2), and
wherein the neighborhood cells are contiguously adjacent to the nearest cell and selected based on being within a distance proximity range from the particular element (page 1, column 1);
generating a cell-to-elements mapping that maps, to each of the cells, a subset of the elements, wherein the subset of the elements mapped to a particular cell in the grid includes those elements in the sequence that are mapped to the particular cell by the element-to-cells mapping; and
using the cell-to-elements mapping to determine, for each of the cells, a nearest element in the sequence, wherein the nearest element to a particular cell is determined based on distances between the particular cell and the elements in the subset of the elements (page 4, column 2, Section “Local box Featurization”, paragraph 2).
Furthermore, Torng et al. teaches a computer-implemented method, as indicated by a method comprising the use of convolutional neural networks (Abstract).
Regarding claim 2, the claim is directed to the matching the element coordinates of the particular element to the cell coordinates further including truncating a decimal portion of the element coordinates to generate truncated element coordinates. Torng et al. teaches the method of claim 1. Torng et al. also teaches truncating the voxel coordinates to 0 or 1 (page 4, column 2, Section “Local box Featurization”.
Regarding claim 3, Torng et al. teaches the method of claim 2. Torng et al. also teaches matching the truncated coordinate values for the first, second, and third dimension (page 4, column 2, Section “Local box Featurization”, paragraph 1) and applying Gaussian filters to the discrete counts to approximate atom connectivity, wherein the standard deviation of the Gaussian filter is calibrated to the average Van der Waal radii of the four atom types (page 4, column 2, Section “Local box Featurization”, paragraph 2).
Regarding claim 4, the claim is directed to the distances being calculated between cell coordinates of the particular cell and element coordinates of the elements in the subset of the elements. Torng et al. teaches the method of claim 1. Torng et al. also teaches the distances being calculates between the cell coordinates and the elements coordinates of the subset of atoms (page 4, column 1).
Regarding claim 5, the claim is directed to the sequence being a protein sequence of amino acids. Torng et al. teaches the method of claim 1. Torng et al. also teaches the sequence being a protein sequence of amino acids (Abstract).
Regarding claim 6, the claim is directed to the elements being atoms of the amino acids. Torng et al. teaches the method of claim 5. Torng et al. also teaches the elements being atoms of the amino acids (Abstract).
Regarding claim 7, Torng et al. teaches the method of claim 1. Torng et al. anticipates the claimed invention and computational method of generating cell mappings and determining nearest elements for atoms of amino acids, and thus inherently teaches the runtime complexity of O(a*f+v).
Regarding claim 8, the claim is directed to the atoms including alpha carbon atoms. Torng et al. teaches the method of claim 7. Torng et al. teaches generating a gridding that covers the whole structure including Carbon bonds, and thus includes alpha carbon atoms (page 4, column 1).
Regarding claim 11, the claim is directed to the cells being three-dimensional voxels. Torng et al. teaches the method of claim 1. Torng et al. also teaches the cells being three-dimensional voxels (page 4, column 2, Section “Local box Featurization”).
Regarding claim 12, the claim is directed to the cell coordinates being three-dimensional coordinates. Torng et al. teaches the method of claim 11. Torng et al. also teaches the cell coordinates being three-dimensional (page 4, column 1).
Regarding claim 13, the claim is directed to the element coordinates being three-dimensional coordinates. Torng et al. teaches the method of claim 12. Torng et al. also teaches the element coordinates being three-dimensional coordinates (page 4, column 1).
Regarding claim 16, the claim is directed to the sequence including M elements, wherein the subset of the elements includes N elements, and wherein M>>N. Torng et al. teaches the method of claim 1. Torng et al. also teaches the sequences including 20 amino acids (Abstract), and teaches the subset of atoms analyzed comprising a 10 voxel grid size (page 4, column 1).
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 1-8, 11-13, and 16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7 and 19 of U.S. Patent No. 12444482. Although the claims at issue are not identical, they are not patentably distinct from each other over the disclosure of the patent which renders the instant claim limitations obvious.
Instant Claims
Patent ‘482
Claim(s)
Claim(s)
1
A computer-implemented method of efficiently determining which elements of a sequence are nearest to uniformly spaced cells in a grid, wherein the elements have element coordinates, and the cells have dimension-wise cell indices and cell coordinates, including: generating an element-to-cells mapping that maps, to each of the elements, a subset of the cells, wherein the subset of the cells mapped to a particular element in the sequence includes a nearest cell in the grid and one or more neighborhood cells in the grid, wherein the nearest cell is selected based on matching element coordinates of the particular element to the cell coordinates, and wherein the neighborhood cells are contiguously adjacent to the nearest cell and selected based on being within a distance proximity range from the particular element; generating a cell-to-elements mapping that maps, to each of the cells, a subset of the elements, wherein the subset of the elements mapped to a particular cell in the grid includes those elements in the sequence that are mapped to the particular cell by the element-to-cells mapping; and using the cell-to-elements mapping to determine, for each of the cells, a nearest element in the sequence, wherein the nearest element to the particular cell is determined based on distances between the particular cell and the elements in the subset of the elements.
19
A computer-implemented method comprising: utilizing a voxelizer to access a three-dimensional structure of a reference amino acid sequence of a protein, and fits a three-dimensional grid of voxels on atoms in the three-dimensional structure on an amino acid-basis to generate amino acid-wise distance channels, wherein each of the amino acid-wise distance channels has a three-dimensional distance value for each voxel in the three-dimensional grid of voxels, and wherein the three-dimensional distance value specifies a distance from a corresponding voxel in the three-dimensional grid of voxels to atoms of a corresponding reference amino acid in the reference amino acid sequence; utilizing an alternative allele encoder to encode an alternative allele amino acid to each voxel in the three-dimensional grid of voxels, wherein the alternative allele amino acid is a three-dimensional representation of a one-hot encoding of a variant amino acid expressed by a variant nucleotide; utilizing an evolutionary conservation encoder to encode an evolutionary conservation sequence to each voxel in the three-dimensional grid of voxels, wherein the evolutionary conservation sequence is a three-dimensional representation of amino acid-specific conservation frequencies across a plurality of species, and wherein the amino acid-specific conservation frequencies are selected in dependence upon amino acid proximity to the corresponding voxel; and utilizing a tensor generator to generate a tensor that includes the amino acid-wise distance channels encoded with the alternative allele amino acid and respective evolutionary conservation sequences.
4
wherein the distances are calculated between cell coordinates of the particular cell and element coordinates of the elements in the subset of the elements
19
wherein each of the amino acid-wise distance channels has a three-dimensional distance value for each voxel in the three-dimensional grid of voxels, and wherein the three-dimensional distance value specifies a distance from a corresponding voxel in the three-dimensional grid of voxels to atoms of a corresponding reference amino acid in the reference amino acid sequence
5
wherein the sequence is a protein sequence of amino acids
19
of a reference amino acid sequence of a protein
6
wherein the elements are atoms of the amino acids
19
a three-dimensional grid of voxels on atoms
8
wherein the atoms include alpha carbon atoms
7
wherein the reference amino acids have alpha-carbon atoms, wherein the three-dimensional distance values correspond to nearest-alpha-carbon atom distances from the corresponding voxel centers to nearest alpha-carbon atoms of corresponding reference amino acids in the reference amino acid sequence
11
wherein the cells are three-dimensional voxels
19
fits a three-dimensional grid of voxels on atoms in the three-dimensional structure on an amino acid-basis
12
wherein the cell coordinates are three-dimensional coordinates
19
wherein each of the amino acid-wise distance channels has a three-dimensional distance value for each voxel in the three-dimensional grid of voxels, and wherein the three-dimensional distance value specifies a distance from a corresponding voxel in the three-dimensional grid of voxels to atoms of a corresponding reference amino acid in the reference amino acid sequence
13
wherein the element coordinates are three-dimensional coordinates
19
wherein each of the amino acid-wise distance channels has a three-dimensional distance value for each voxel in the three-dimensional grid of voxels, and wherein the three-dimensional distance value specifies a distance from a corresponding voxel in the three-dimensional grid of voxels to atoms of a corresponding reference amino acid in the reference amino acid sequence
With regard to claims 2 and 3, although the claims of patent ‘482 are silent with regard to limitations of “truncating a decimal portion of the element coordinate”, the Specification of the Patent discloses in column 68, line 13, truncating the decimal portion of the element coordinates, and matching a first, second, and third truncated element coordinate as recited in instant claim 3.
With regard to claim 7, although the claims of patent ‘482 are silent with regard to the runtime complexity, the Specification of the Patent discloses in column 30, line 4, a runtime complexity of O(atoms*attributes+voxels), and in column 68, line 52, discloses a runtime complexity of O(a*f+v) with respect to the number of atoms, number of amino acids, and number of cells.
With regard to claim 16, although the claims of patent ‘482 are silent with regard to the limitation of “the sequence includes M elements, wherein the subset of the elements includes N elements, and wherein M>>N”, the Specification of the Patent discloses in column 69, line 20, that the sequence includes M elements, wherein the subset of the elements includes N elements, and wherein M>N.
Thus, the instant claims are obvious over the claims and disclosure of Patent ‘482.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686