Full opinion text
FINDINGS OF FACT AND CONCLUSIONS OF LAW JORDAN, District Judge. TABLE OF CONTENTS I. INTRODUCTION.........................................................303 II. FINDINGS OF FACT......................................................303 A. The Parties ...........................................................303 B. Technological Background ..............................................303 1. Alpha-Amylases....................................................303 2. Protein Engineering................................................304 3. Claims of the ’031 Patent............................................305 C. Prosecution History of the ’031 Patent....................................306 1. The Original Claims ................................................306 2. The First Office Action..............................................307 a. Written Description and Enablement..............................307 b. Obviousness....................................................308 3. Novozymes’s Response..............................................308 4. The Second Office Action............................................309 5. Evidence of Unexpected Results......................................310 6. Allowance.........................................................311 D. The Machius Reference.................................................312 E. Marketing of Spezyme Ethyl............................................313 F. Amino Acid Sequences of Spezyme Ethyl and G997.........................313 III. CONCLUSIONS OF LAW..................................................315 A. Claim Construction.....................................................315 1. “Bacillus stearothermophilus Alpha-Amylase”.........................317 a. The Parties’ Proposed Constructions..............................317 b. The Court’s Construction........................................317 i. The Term is Not Limited to SEQ ID NO:3.....................317 ii. The Term is Not Limited to Proteins of a Particular Length.....318 2. “% Homology”.....................................................319 a. The Parties’ Proposed Constructions..............................319 b. The Court’s Construction........................................319 B. Infringement..........................................................321 1. Claim 1 ...........................................................321 2. Claim 3 ...........................................................322 3. Claim 5 ...........................................................322 C. Invalidity.............................................................322 1. Obviousness.......................................................323 a. Suzuki and Bisg°ard-Frantzen ...................................323 b. Unexpected Results.............................................324 i. Suzuki Conditions..........................................324 ii. Experimental Procedures....................................325 iii. Expected Results...........................................327 c. Machius.......................................................328 2. Enablement .......................................................329 D. Unenforceability.......................................................330 1. Inequitable Conduct................................................330 a. The Borchert Declaration........................................331 b. Failure to Disclose the Machius Reference.........................332 2. Prosecution Laches.................................................333 IV. SUMMARY OF CONCLUSIONS..... ......................................333 I. INTRODUCTION This is a patent infringement case. No-vozymes A/S (“Novozymes”) has sued Genencor International, Inc. (“Genencor”) and Enzyme Development Corporation (“EDC”) (collectively “Defendants”), alleging infringement of U.S. Patent No. 6,867,031 (issued Mar. 15, 2005) (the “ ’031 patent”). Trial of this matter has been bifurcated: a bench trial on patent infringement, invalidity, and unenforceability was held from March 6 to March 9, 2006, and a second bench trial on willfulness and damages is scheduled to begin on October 10, 2006. The following, issued pursuant to Federal Rule of Civil Procedure 52(a), are my findings of fact and conclusions of law as to the liability issues tried last March. For the reasons that follow, including my decision on claim construction, I conclude that Defendants have infringed claims 1, 3, and 5 of the ’031 patent, that those claims are valid, and that the ’031 patent is enforceable. Accordingly, this case will proceed to the second phase trial to decide the issues of willfulness and damages. II. FINDINGS OF FACT A. The Parties 1. Novozymes is a Danish corporation with a place of business in Bagsvaerd, Denmark. (Uncontested Facts, Docket Item [“D.I.”] 101 at ¶ III.A.) Novozymes is the sole assignee of the ’031 patent titled “Amylase Variants.” (’031 patent.) 2. Genencor is a Delaware corporation having a principal place of business in Palo Alto, California. (Uncontested Facts, D.I. 101 at ¶ III.B.) Genencor sells an alpha-amylase product under the brand name Spezyme® Ethyl. (Id. at ¶ III.V.) 3. EDC is a Delaware corporation having a principal place of business in New York, New York. (Id. at ¶ III.C.) EDC is a United States distributor of Genencor’s Spezyme Ethyl. (Id. at ¶ III.W.) B. Technological Background 1. Alpha-Amylases 4. The ’031 patent relates to alpha-amylase enzymes. (’031 patent, 1:21-22.) Enzymes are catalysts, meaning that they increase the rate of chemical reactions. (Uncontested Facts, D.I. 101 at ¶ III.E; Arnold, D.I. 120, Trial Transcript [“Tr.”] at 143:15-144:1.) The alpha-amylase enzymes described by the ’031 patent are proteins (Arnold, Tr. at 139:4-6) that catalyze the breakdown of alpha-1,4-glucosidic bonds (Uncontested Facts, D.I. 101 at ¶ III.E). Alpha-1,4-glucosidic bonds connect individual glucose molecules together to form starch molecules. (Id.) By breaking those bonds, alpha-amylases “break apart the starch complexes and convert complex starch into smaller, simpler groups of glucose molecules ____” (Id.) 5. “[A]lpha-amylases are useful in a variety of commercial applications that involve the processing of starches [,including] ... the fuel ethanol industry, where ethanol fuel is produced from starch-rich crops such as corn, barley, and wheat.” (Id. at ¶ III.G.) “Alpha-amylases are used in the fuel ethanol industry to liquefy and reduce the viscosity of starch feedstocks so that they are easier to process in the manufacturing plant.” (Id. at ¶ III.H.) 6. In the process of fuel ethanol production, alpha-amylases are typically added to a starch slurry that is subjected to temperatures above 100°C for up to ten minutes, followed by an incubation at 80°C for a few hours. (Borchert, Tr. at 25:8-15.) Hence, the thermostability of the enzyme, its capacity to withstand high temperatures, is important to its effectiveness in industrial applications. (See id. at 25:19-26:4.) By using alpha-amylases with better thermostability, manufacturers can use less of the enzyme and reduce costs. (Id. at 26:5-9, 29:12-20.) 7. One way to improve the thermosta-bility of alpha-amylases is to add high levels of calcium to the starch slurry. (Id. at 26:15-22.) But high calcium levels interfere with later processing, so that the calcium has to be removed, an additional step that is inconvenient and increases costs. (Id. at 26:25-27:14, 29:18-20.) 8. The ’031 patent is directed at alpha-amylases, produced by protein engineering, that are thermostable in industrial applications, without the need for added calcium. (Id. at 26:5-11; see generally ’031 patent, 9:48-11:65.) 2. Protein Engineering 9. Like all proteins, alpha-amylases are polymers composed of amino acids linked together by peptide bonds into a linear chain. (Uncontested Facts, D.I. 101 at ¶ III.I.) Each protein chain includes many amino acids assembled in a particular order, so that a particular protein may be identified by its ordered sequence of amino acids. (Id.) That ordered sequence is referred to as the protein’s “amino acid sequence” or its “primary structure.” (Id.) 10. “One end of a protein chain of amino acids is called the ‘N-terminus,’ and the other end is called the ‘C-terminus.’ ” (Id. at ¶ III.J.) Scientists write an amino acid sequence by listing the amino acids in order from the N-terminus to the C-terminus, using one-letter codes for each of the twenty naturally occurring amino acids. (Id. at ¶ III.K) For example, the amino acid alanine has the one-letter code “A”, and asparagine has the one-letter code “N”. (’031 patent, 6:44-47.) Protein sequences written using the one-letter codes are disclosed in the ’031 patent. (Id. at Fig. 1.) 11. “It can be informative when comparing proteins to compare their respective amino acid sequences.” (Uncontested Facts, D.I. 101 at ¶ III.N.) The amino acid sequences are typically “aligned” with one another to achieve a visual correspondence of individual amino acids or groups of amino acids that are common to the proteins being compared. (Id.) Once sequences are aligned, the percentage of identical amino acid mátches in the aligned proteins can be calculated and reported as a percent of “identity,” also referred to at times as “homology.” (Id. at ¶ III.O.) Generally, the alignments and calculations may be done using computer software. (’031 patent, 4:36-45; Devereux, Tr. at 103:20-104:4, 106:11-107:2 (briefly describing the use of software to align protein sequences).) 12. The function of a protein and the conditions under which it can perform that function are determined at least in part by the protein’s amino acid sequence. (Uncontested Facts, D.I. 101 at ¶ III.M.) That is because a particular linear chain of amino acids will fold into a characteristic three-dimensional structure. (Borchert, Tr. at 21:1-7.) The so-called “tertiary” structure of a protein describes the relative positions in three-dimensional space of the protein’s atoms. (Machius, Tr. at 456:13-19.) That tertiary structure is the specific overall shape of the protein (id. at 456:13-15), which determines the protein’s function (id. at 457:15-22). 13. Because of the relationship between protein sequence, structure, and function, one can alter the function or other properties of a protein by altering its sequence. Protein engineering is “the deliberate modification of the amino acid sequence of [a] protein,” so that the protein’s properties can be studied or improved. (Arnold, Tr. at 135:16-21.) Protein sequences can be modified by making substitutions, insertions, or deletions of amino acids in the sequence. (Borchert, Tr. at 23:12-13.) 14. Protein engineers modify a protein sequence by changing the DNA sequence of the gene that encodes that protein. (Al-ber, Tr. at 202:23-203:11; Arnold, Tr. at 139:21-140:5.) Each amino acid in a protein sequence corresponds to a triplet of nucleotides in the DNA sequence of the corresponding gene. (Alber, Tr. at 202:25-203:3.) The DNA sequence may be modified “very precisely” (id. at 203:5-6), thus allowing the modification of protein sequences. 3. Claims of the ’031 Patent 15. Novozymes is asserting claims 1, 3, and 5 of the ’031 patent. (See, e.g., D.I. 118 at 22-26.) Those claims relate to alpha-amylases originally found in a species of bacteria named Bacillus stearothermo-philus but then engineered for improved thermostability. (’031 patent, 65:11-17, 65:21-66:12, 66:16-19.) 16. Specifically, claims 1, 3, and 5 relate to alpha-amylases that have two particular amino acids deleted, those at positions 179 and 180, using the numbering of a reference Bacillus stearothermophilus alpha-amylase sequence given in the patent, “SEQ ID NO:3.” (’031 patent, 65:11-17, 65:21-66:12, 66:16-19.) Those alpha-amylases have improved thermostability without the need for calcium as an added support at high temperature. (Borchert, Tr. at 26:5-11; ’031 patent, 9:48-59, 9:62-66,10:40-48,11:41-65.) 17. Claim 1 of the ’031 patent reads: A variant of a parent Bacillus stearoth-ermophilus alpha-amylase, wherein the variant has an amino acid sequence which has at least 95% homology to the parent Bacillus stearothermophilus alpha-amylase and comprises a deletion of amino acids 179 an [sic] 180, using SEQ ID NO:3 for numbering, and wherein the variant has alpha-amylase activity. (’031 patent, 65:11-17.) 18. Claim 3 reads: A variant alpha-amylase, wherein the variant has at least 95% homology to SEQ ID NO:3 and comprises a deletion of amino acids 179 and 180, using SEQ ID NO:3 for numbering and wherein the variant has alpha-amylase activity. (Id. at 65:21-66:12.) 19. Claim 5 reads: A variant of a Bacillus stearothermophi-lus alpha-amylase, wherein the alpha-amylase variant consists of a deletion of amino acids 179 and 180, using SEQ ID NO:3 for numbering. (Id. at 66:16-19.) C. Prosecution History of the ’031 Patent 20. The application that issued as the ’031 patent, Application No. 10/025,648 (the “ ’648 application”), was filed on December 19, 2001. (’031 patent, cover page.) The ’648 application was filed as a division of Application No. 09/902,188, filed July 10, 2001, which was a continuation of Application No. 09/354,191, filed July 15, 1999, which was a continuation of Application No. 08/600,656, filed February 13, 1996, which was a continuation of International Application No. PCT/DK96/00056, filed February 5, 1996. (Id.) The ’648 application claimed priority to a group of four Danish patent applications filed from February 3 to October 6, 1995. (Id.) To support an effective filing date for a United States patent, a foreign priority application must provide a sufficient written description of what is claimed in the United States patent. In re Gosteli, 872 F.2d 1008, 1010-11 (Fed.Cir.1989). The earliest of the four Danish applications that discloses a Bacillus stearothermophilus alpha-amylase is the one that was filed on March 29, 1995, Application No. PA 1995 00336. (Trial Exhibit [“TX”] 101, D.I. 121 at [ A-XXXX-XXXX ].) Thus, according to Defendants (D.I. 115 at 4-5, ¶¶ 22-23), no earlier Danish application will support an effective filing date for the ’031 patent, and the earliest possible effective filing date for that patent is March 29,1995. 1. The Onginal Claims 21. A preliminary amendment to the ’648 application was filed on December 19, 2001. (TX 101, D.I. 121 at A-7045-48.) That amendment canceled claims 1-29 and added 18 new claims, numbered 30-47. (Id.) New claims 30-39 were directed to alpha amylases, and claims 40-47 were directed to DNA, vectors, host cells, and methods of expressing the alpha-amylases. (Id.) 22. Claim 30 was an independent claim that read: A variant of a parent alpha-amylase enzyme, wherein said parent alpha-amylase has an amino acid sequence which has at least 80% homology to SEQ ID NO:3, and wherein said variant comprises deletions at positions equivalent to positions 179 and 180 in SEQ ID NO:3 (using SEQ ID NO:3 for numbering). (Id. at A-7045.) 23. Claims 31-34 depended directly from claim 30. (Id. at A-7045-46.) Claims 31-33 specified the homology between the parent alpha-amylase amino acid sequence and SEQ ID NO:3 as at least 85%, 90%, and 95% respectively. (Id. at A-7045.) Claim 34 claimed “[t]he variant of claim 30, wherein the variant further comprises amino acid substitutions of a cysteine at positions equivalent to positions 349 and 428 in SEQ ID NO:3.” (Id. at A-7046.) 24. Claim 35 was an independent claim that read: An isolated alpha-amylase enzyme comprising an amino acid sequence having an amino acid sequence which has at least 80% homology to SEQ ID NO:3, modified by having deletions at positions equivalent to positions 179 and 180 in SEQ ID NO:3. (Id.) 25. Claims 36-39 depended directly from claim 35. (Id.) Claim 36 claimed “[t]he alpha-amylase enzyme of claim 35, wherein said alpha-amylase enzyme is further modified by having amino acid substitutions of a cysteine at positions equivalent to 349 and 428 in SEQ ID No:3.” (Id.) Claims 37-39 specified the homology between the alpha-amylase amino acid sequence and SEQ ID NO:3 as at least 85%, 90%, and 95% respectively. (Id.) 2. The First Office Action 26. The examiner issued an office action on July 29, 2003. (Id. at A-7619-29.) After a restriction requirement, the applicants elected to prosecute claims 30-39. (Id. at A-7621, A-7636.) a. Written Description and Enablement 27. The examiner rejected claims 30-34 for failing to meet the written description requirement of 35 U.S.C. § 112. (Id. at A-7623.) According to the examiner, the specification only described a few representative species of the genus of enzymes that were included in the scope of claims 30-34. (Id.) As written, those claims included variant enzymes “with any number of alterations of the parent enzyme as long as amylase activity is maintained.” (Id.) Given that scope, the specification failed to sufficiently describe the invention so that a skilled artisan would recognize that the applicants were in possession of the invention. (Id.) 28. The examiner also rejected claims 30-34 under 35 U.S.C. § 112, because the specification did not enable one skilled in the art to practice the full scope of the claims. (Id. at A-7624-27.) While claims 30-34 required the parent alpha-amylases to have at least 80% homology to SEQ ID NO:3, the variants were not so limited. (Id. at A-7624.) The claims covered variants “with any number of alterations of the parent enzyme as long as amylase activity is maintained,” and as long as the alterations included the deletions of the two amino acids at positions equivalent to 179 and 180 in SEQ ID NO:3. (Id.) Considering the number of possible variants, the unpredictability of the art of protein engineering, and the lack of any detailed instruction as to which regions of the alpha-amylase enzymes could be modified without destroying the alpha-amylase activity, the examiner concluded that the specification did not enable one to make variants with any number of alterations relative to the parent. (Id. at A-7625-27.) 29. The examiner noted that the written description and enablement rejections for claims 30-34 would be overcome if claim 30 was amended so that the class of claimed variants were required to have “at least 80% sequence identity to SEQ ID NO:3.” (Id. at A-7627.) b. Obviousness 30. The examiner rejected claims 30-33, 35, and 37-39 under 35 U.S.C. § 103(a) as obvious in light of two references. (Id. at A-7627-28.) 31. The first reference (“the Suzuki reference” or “Suzuki”), titled “Amino Acid Residues Stabilizing a Bacillus a-Amylase against Irreversible Thermoinactivation” and authored by Suzuki et al., was published in the Journal of Biological Chemistry in 1989. (TX 115, D.I. 122 at A-8233-38.) Suzuki disclosed alpha-amylases from Bacillus amyloliquefaciens that were modified by the deletion of two amino acids at positions 176 and 177. (Id. at A-8233, A-8237-38.) Alpha-amylases with those deletions had better thermostability. (Id. at A-8237-38.) 32. The second reference (“the Bisgárd-Frantzen reference” or “Bisgárd-Frantzen”) was a patent application, Publication No. WO 95/10603, published April 20, 1995 and titled “Amylase Variants.” (TX 177, D.I. 122 at A-8403-507.) Bisgárd-Frantzen disclosed that the alpha-amylases of Bacillus amyloliquefaciens, Bacillus stearothermophilus, and Bacillus licheniformis were “highly homologous on the amino acid level.” (Id. at A-8413-14.) A sequence alignment of those alpha-amy-lases showed that positions 176 and 177 of the Bacillus amyloliquefaciens enzyme corresponds to positions 179 and 180 of the Bacillus stearothermophilus enzyme. (Id. at A-8415-16.) 33. According to the examiner, “it would have been obvious to one of ordinary skill in the art to introduce the [deletions] disclosed by Suzuki ... into the corresponding positions [179 and 180] of Bacillus stearothermophilus a-amylase,” in order to increase its thermostability. (TX 101, D.I. 121 at A-7628.) Because of the similarity between the Bacillus amylo-liquefaciens and Bacillus stearothermo-philus alpha-amylases revealed by Bisgárd-Frantzen, one of ordinary skill in the art would, the examiner concluded, reasonably expect that the change in the Bacillus stearothermophilus alpha-amylase would give similar results as those disclosed by Suzuki for the Bacillus amy-loliquefaciens alpha-amylase. (Id.) 3. Novozymes’s Response 34. On January 13, 2004, Jason Gar-bell, an in-house patent attorney for Novo-zymes (Garbell, Tr. at 4:13-17), sent an email message to a group at Novozymes, including the inventors of the ’031 patent, commenting on the examiner’s obviousness rejection. (TX 110, D.I. 122 at A-8169-70.) In that e-mail, Mr. Garbell proposed two options for responding to the rejection: “Option 1” was to show by experiment that the claimed deletion in Bacillus stearothermophilus alpha-amylase yielded unexpected results, and “Option 2” was to add limitations to the rejected claims such as those in claims 34 and 36, which were not rejected for obviousness. (Id. at A-8170.) Mr. Garbell preferred Option 1, because that would not require narrowing the scope of the claims and would limit the design-around opportunities available to competitors. (Id.) Genencor was known to be one of those competitors. (Id. at A-8169 (referring to Genencor as GCI); Borchert, Tr. at 355:8-356:15.) 35. Mr. Garbell needed to respond to the office action by January 29, 2004 (TX 110, D.I. 122 at A-8170), and the scientists at Novozymes informed him that the experimental work required for Option 1 could not be completed by then (id. at A-8169, A-8171). It was suggested that proceeding with Option 2 would “give time” for carrying out the experiments, which might then support broader claims. (Id. at A-8169.) 36. On January 14, 2004, the applicants filed an amendment. (TX 101, D.I. 121 at A-7632-37.) In response to the obviousness rejection, claims 34 and 36 were canceled, and independent claims 30 and 35 were amended to add the limitations of claims 34 and 36, respectively. (Id. at A-7634, A-7637.) 37. In response to the written description and enablement rejections, the applicants amended claim 30 to recite that the variant “has at least 80% identity to said parent alpha-amylase.” (Id. at A-7634, A-7636-37.) 4. The Second Office Action 38. The examiner issued another office action on April 6, 2004. (Id. at A-7717-27.) The obviousness rejection was withdrawn. (Id. atA-7719.) 39. The examiner maintained the rejection of claims 30-33 for failure to meet the written description requirement. (Id. at A-7719-21.) Again, the examiner said that the specification described only a few of the many alpha-amylases covered by those claims, so that one skilled in the art could not conclude that the applicants had possession of the claimed invention. (Id. at A-7720-21.) The examiner suggested that the claims be narrowed by requiring the variants to have alpha-amylase activity. (Id. atA-7721.) 40. The examiner rejected claims 30-33, 35, and 37 for failure to meet the enablement requirement. (Id. at A-7721-26.) While the applicants had stated in their response to the first office action that claim 30 had been amended following the examiner’s suggestion (id. at A-7636-37), the examiner noted that the applicants “did not in fact amend the claim exactly as suggested” (id. at A-7725). Rather than requiring the variant to have at least 80% identity to SEQ ID NO:3, as the examiner had suggested (Finding of Fact [“FF”] ¶ 29), the applicants amended claim 30 to require the variant to have at least 80% identity to the parent alpha-amylase (FF ¶ 37). However, the examiner acknowledged that the amendment was “similar” to her suggestion. (TX 101, D.I. 121 at A-7725.) Still, while the examiner recognized that the scope of claims 30-33 had been narrowed, “upon further reconsideration” she believed that the specification did not enable one of ordinary skill to make variants with at least 80% identity to the parent without undue experimentation. (Id.) As in the first office action, the examiner noted the large number of possible variants, the unpredictability of the art, and the lack of guidance about which regions of the alpha-amylases could be modified without losing enzyme activity. (Id. at A-7721-26.) Claims 35 and 37, which required the variant to have at least 80% and 85% homology to SEQ ID NO:3, respectively, were also not supported by an enabling disclosure, the examiner concluded. (Id.) 41. The examiner noted that the specification was enabling for alpha-amylases “having at least 90% homology to SEQ ID NO:3” and having the claimed modifications. (Id. at A-7721.) Thus, claims 38 and 39, which required at least 90% or 95% homology to SEQ ID NO:3, respectively, would be allowable, the examiner indicated, if they were rewritten in independent form. (Id. at A-7726.) 5. Evidence of Unexpected Results 42. In an interview on September 3, 2004, Mr. Garbell and Dr. Borchert discussed with the examiner the obviousness rejection from the first office action. (Id. at A-7798-99.) The examiner stated that she was shown a draft declaration that “appear[ed] to show results sufficiently unexpected to overcome” the previous obviousness rejection. (Id. at A-7799.) Those unexpected results were later submitted to the examiner in the form of a declaration under 37 C.F.R. § 1.132, dated September 6, 2004 (the “Borchert Declaration”). (Id. at A-7739-56.) 43. The Borchert Declaration described the results of an experiment comparing the thermostability of Bacillus stearothermophilus alpha-amylase (“BSG”), with and without deletion of residues179 and 180, and Bacillus amy-loliquefaciens alpha-amylase (“BAN”), with and without deletion of residues 176 and 177. (Id. at A-7739, ¶ 3.) BAN was the alpha-amylase studied by Suzuki. (FF ¶ 31.) 44. Genes for the variants of BSG and BAN with their respective deletions (“BSGdel” and “BANdel” respectively) were constructed by standard methods and the gene sequences were confirmed by DNA sequencing. (TX 101, D.I. 121 at A-7740, ¶ 4.) Cells producing each of the four enzymes, BSG, BSGdel, BAN, and BAN-del, were grown under identical conditions, and the alpha-amylases were separated from the cells by centrifugation. (Id. at A-7740, ¶ 5.) The alpha-amylase-containing supernatants were diluted in buffer containing 0.1 mM calcium and incubated at 80°C in a PCR machine, and at various times the alpha-amylase activity was measured. (Id.) According to the Borchert Declaration, the incubation temperature of 80°C was “the highest temperature where [all four alpha-amylases] could be reliably compared.” (Id.; see also Borchert, Tr. at 686:8-688:17 (describing the calibration experiments to determine the temperature at which all four enzymes would yield reliable measurements).) 45. The alpha-amylase activity of each sample was measured at various times, and the results were reported in tabular form as a percentage residual activity at each time. (TX 101, D.I. 121 at 7741-42, ¶ 6.) BSGdel maintained its activity for the longest period of time: 61% residual activity was measured at 4200 minutes, the last time point of the experiment. (Id.) 46. Four data points were omitted before the data were analyzed. First, two measurements for BSGdel taken at 2881 minutes were omitted by a Novozymes lab technician, Vibeke Holbo, because she noted that the sample used for those measurements had evaporated during incubation. (Holbo, Tr. at 671:3-14; Borchert, Tr. at 384:22-385:2, 412:17-24.) Two other measurements for BSGdel taken at 2940 minutes were omitted by Dr. Borchert, because he noted that the measurements “were extremely far apart” and one showed activity above 130%. (Borchert, Tr. at 386:9-15, 412:25-413:2, 414:8-17.) Dr. Borchert decided that he could not “with any confidence include such measurements in the data analysis.” (Id. at 414:16-17.) 47. A regression analysis was conducted for each data series, and the half-life for each alpha-amylase, i.e. the time at which the alpha-amylase had half of its original activity (Klibanov, Tr. at 515:18-25), was calculated. (TX 101, D.I. 121 at A-7742, ¶ 7.) The four half-lives were: BAN, 0.9 minutes; BANdel, 9.5 minutes; BSG, 92 minutes; BSGdel, 5775 minutes. (Id.) Based on those numbers, Dr. Borchert reported that the deletion of residues 176 and 177 in BAN improved thermostability 11-fold, and the corresponding deletion of residues 179 and 180 in BSG improved thermostability 63-fold. (Id.) Thus, the thermostability was improved 5.7 times as much in BSG as in BAN (63/11=5.7). (Id.) 48. According to Dr. Borchert, the deletion in BSG “has a pronounced and very surprising effect on the thermal stability.” (Id. at A-7743, ¶ 9.) “[The] results are statistically significant and very surprising as the effect of the double deletion in BSG is significantly greater than what would have been expected based on the combined teachings of Suzuki ... in view of Bis-gaard-Frantzen .... ” (Id. at A-7743-44, ¶ 9.) 6. Allowance 49. After the interview on September 3, the applicants submitted an amendment dated September 6, 2004 (id. at A-7733-56) that cancelled all the pending claims and added five new claims, numbered 48-52 (id. at A-7734). For claims 48, 50, and 52, the applicants removed the requirement for cysteine substitutions at positions 349 and 428, which had been added in response to the obviousness rejection from the first office action. (Id.) According to the applicants, an obviousness rejection based on Suzuki and Bisgárd-Frantzen, if it were reasserted by the examiner in response to the broadened claims, would be overcome by the evidence of unexpected results in the Borchert Declaration. (Id. at A-7736-37.) 50. In response to the earlier enablement and written description rejections, the applicants drafted claims 48-49 and 50-51 to require the variants to have at least 95% homology to the parent Bacillus stearothermophilus alpha-amylase and to SEQ ID NO:3, respectively, and to have alpha-amylase activity. (Id. at A-7734-36.) As to the enablement rejection, the applicants noted the examiner’s suggestion that the claims would be enabled if they required the variants to have at least 90% homology to SEQ ID NO:3. (Id. at A-7735-36; see FF ¶41.) The applicants argued that the enablement rejection was “rendered moot by the new claims as the new claims recite a homology of 95%.” (TX 101, D.I. 121 at A-7736.) 51. On September 21, 2004, the examiner issued a notice of allowance. (Id. at A-7791-97.) In her remarks, the examiner stated that the Borchert Declaration “establishes that the claimed variants exhibit unexpectedly large increases in ther-mostability when compared to the increases in thermostability obtained for the corresponding mutations taught by Suzuki et al. As such the claimed variants are non-obvious over the prior art.” (Id. at A-7796.) The examiner made no remarks concerning the written description and enablement rejections. (Id.) 52. Claims 48-52, submitted by the applicants on September 6, 2004, correspond to claims 1-5, issued without further amendment as the claims of the ’031 patent. (Compare id. at A-7734 with ’031 patent, 65:10-66:19.) D. The Machius Reference 53. Another reference relating to alpha-amylases that was the subject of repeated emphasis during trial is entitled “Crystal Structure of Calcium-depleted Bacillus lichenifomiis a-amylase at 2.2 <A Resolution,” and was authored by Ma-chius et al. and published in the Journal of Molecular Biology at least as early as March 13, 1995. (TX 173, D.I. 122 at A-8375-90; “the Machius reference”.) The applicants did not disclose the Machius reference to the examiner during prosecution of the ’648 application. (Garbell, Tr. at 11:22-12:6, 429:2-6; Borchert, Tr. at 372:7-15.) 54. That reference reports the three-dimensional structure of a calcium-free form of Bacillus lichenifomiis alpha-amylase (“BLA”) as determined using x-ray crystallography. (TX 173, D.I. 122 at A-8376, Abstract.) The Machius reference discusses the thermostability of alpha-amylases, including BAN and BSG, in the context of the three-dimensional structure of BLA. (Id. at A-8382-85, A-8387.) First, the reference showed a sequence alignment of BLA, BAN (which the reference referred to as “BAA”), and BSG (which the reference referred to as “BstA”), along with the secondary structure elements of BLA determined from the three-dimensional structure. (Id. at A-8383-84, A-8387, Fig. 7.) The Machius reference stated that “[ajccording to the alignment, the three-dimensional structures of [BAN] and [BSG] can be expected to be very similar to that of BLA.” (Id. at A-8384.) While the paragraph leading up to that statement pointed to Figure 7 of the article, which included secondary structure information, the prediction about the similarity of three-dimensional structure between the three alpha-amylases is based, according to its own terms, on the sequence similarity shown by the “alignment.” (Id.; see also Machius, Tr. at 465:15-22, 492:17-21 (stating that, based on sequence similarity, it “would be reasonable to expect” similarity in three-dimensional structure).) That sequence similarity was also disclosed by the Bisgárd-Frantzen reference. (TX 177, D.I. 122 at A-8413, A-8415-16.) 55.Second, the Machius reference specifically discussed, in the context of the BLA structure, the deletions of amino acids 176 and 177 in BAN disclosed by Suzuki. (TX 173, D.I. 122 at A-8384.) The corresponding two amino acids in BLA are shown by Maehius’s three-dimensional structure to be in a loop on the surface of the protein. (Id.) Based on the predicted structural similarity between BLA, BAN, and BSG, the deleted amino acids in BAN and BSG would also be expected to be on surface loops. Because of their position on the surface of the protein, a person having ordinary skill in the art would predict that deleting those amino acids would be less likely to disrupt specific interactions that might vary slightly between BLA, BAN, and BSG. (Machi-us, Tr. at 774:3-22.) According to the reference, the presence of two extra amino acids on the surface loop “could cause increased mobility of this region and a decreased thermostability of the whole protein.” (TX 173, D.I. 122 at A-8384.) 56. The Machius reference does not specifically discuss whether a person having ordinary skill in the art would expect the deletion of residues 179 and 180 in BSG to give improved thermostability, although that conclusion might be drawn from the predicted structural similarity between BSG and BAN. The Machius reference also does not discuss the degree of improvement that might be expected. E. Marketing of Spezyme Ethyl 57. Genencor and EDO began selling the accused product, Spezyme Ethyl, in the United States by April 2004. (Uncontested Facts, D.I. 101 at ¶ III.X.) 58. Genencor sold other alpha-amylas-es before Spezyme Ethyl (Crabb, Tr. at 32:12-18), including one product called — in an apparent homage to the Mertz family of “I Love Lucy” fame — Spezyme Fred (id. at 35:3-9). None of those products had a sufficient combination of acid tolerance, thermostability, and low cost to be economically viable for use in fuel ethanol production. {Id. at 32:19-24.) Some Gen-encor customers demanded an alpha-amylase that was better suited for fuel ethanol production. {Id. at 36:3-22.) Efforts to modify Spezyme Fred did not result in a commercialized product for the fuel ethanol market. {Id. at 38:6-39:11.) 59. Since April 2004, sales of Spezyme Ethyl have been considerable. {See Uncontested Facts, D.I. 101 at ¶ III.Y.) F. Amino Acid Sequences of Spezyme Ethyl and G997 60. The parties agree on the amino acid sequence of Spezyme Ethyl. {Id. at ¶ III.Z.) That sequence is 484 amino acids long, and ends with the following ten amino acids at the C-terminus: VSVWVPRKTT. {Id.; TX 125, D.I. 122 at A-8345.) 61. The gene for Spezyme Ethyl was originally engineered from an alpha-amylase gene from Bacillus stearothermophi-lus strain ATCC No. 39,709. (TX 194 at A-8521.) An alpha-amylase produced from that gene, before the gene was modified to produce Spezyme Ethyl, was sold by Genencor as “G997.” (Crabb, Tr. at 45:16-19, 46:10-13.) One of Genencor’s scientists characterized G997 as a “wild type” Bacillus stearothermophilus product (id. at 40:1-3), a term that means that it is the product of a gene taken from a naturally occurring organism before any modifications are made (Arnold, Tr. at 137:25-138:7). 62. The parties do not agree on the sequence of G997. Specifically, while Novo-zymes presented a single sequence for G997, Defendants argue that there is no single, stable sequence for G997. (D.I. 116 at 10-11.) Instead, according to Defendants, G997 is a mixture of proteins, each of which has a different number of amino acids deleted from the C-terminus, a feature that Defendants contend disqualifies G997 from being a “Bacillus stearothermo-philus alpha-amylase”, as that term is used in claims 1 and 5. See infra Section III.B.l. 63. The amino acid sequence of G997 presented by Novozymes at trial (TX 199, D.I. 122 at A-8529) was determined using mass spectrometry. (Jorgensen, Tr. at 71:16-21; TX 206, D.I. 122 at A-8537-39.2.) At the trial, questions were raised about the provenance of the G997 sample that was analyzed (see Tr. at 74-76), so the parties agreed that a G997 sample would be provided by Genencor at the close of trial (D.I.112). That sample was analyzed by Dr. Jorgensen using the same protocol he used to determine the sequence presented during the trial (TX 206, D.I. 122 at A-8537-39.2), and its amino acid sequence (TX 226, D.I. 122 at A-8556.1) was the same as that presented at trial (TX 199, D.I. 122 at A-8529). The parties have stipulated that the sequence in the exhibit marked “TX 226” is the only sequence of the only alpha-amylase determined by No-vozymes to be present in the G997 sample provided by Genencor. (D.I.112.) That sequence is 486 amino acids long, and ends with the following ten amino acids at the C-terminus: VSVWVPRKTT. (TX 226, D.I. 122 at A-8556.1) 64. Judy Chang, a research associate at Genencor (Crabb, Tr. at 50:13-18), wrote an analytical report dated April 19, 2004 concerning the sequences of G997, Spezyme Ethyl (which was also referred to in the report as “EBS2”), and another alpha-amylase called Termamyl SC. (TX 161, D.I. 122 at A-8365-74.) Ms. Chang reported a single molecular weight for each of the three proteins, determined by mass spectrometry. (Id. at A-8368, Table 2.) The measured molecular weights for all three proteins were less than the “theoretical molecular weight” calculated from the DNA sequence of the respective genes. (Id. at A-8368.) The three proteins were then subjected to digest mapping (id.), a process that yields fragments whose size depends on the particular amino acid sequence of the proteins (id. at A-8366). According to that analysis, “[fjragments were detected which corresponded to the N-terminus for all three enzymes. However, no fragments within 27-29 residues of the C-terminus were found. A truncation of 27-29 amino acids [from the C-terminus] would be consistent with the molecular weights measured for the intact proteins.” (Id. at A-8368-69.) 65. Testifying on behalf of Defendants, Dr. Alber stated that he interpreted Ms. Chang’s report to show multiple sequences for G997, which had different lengths corresponding to deletions of 27, 28, and 29 amino acids from the C-terminus. (Alber, Tr. at 249:13-17, 280:9-19, 291:12-292:8.) Dr. Alber supported that interpretation by pointing to Ms. Chang’s statement about a truncation of “27-29 amino acids” (id. at 280:9-19) and her use of the plural, “molecular weights,” in the description of her results. (Id. at 291:12-292:8.) 66. I conclude that Dr. Alber’s interpretation is incorrect. First, Ms. Chang reports only one measured molecular weight for each of the three proteins analyzed, including one for G997. (TX 161, D.I. 122 at A-8368, Table 2.) Dr. Alber speculates that the reported molecular weight in Table 2 of the report must be just one of several measured for G997 (Alber, Tr. at 289:8-15), but there is no specific support for that in the report. Second, the digest mapping experiment found “no fragments within 27-29 residues of the C-terminus” (TX 161, D.I. 122 at A-8368-69), indicating that the location of the truncation could not be more precisely determined. The discussion of a truncation of 27-29 amino acids thus appears to reflect the realities of the experiment, rather than the detection of multiple proteins with different truncations. Third, Ms. Chang’s reference to “molecular weights” refers to the weights “measured for the intact proteins,” i.e., the three proteins that were analyzed: G997, Spezyme Ethyl, and Termamyl SC. (TX 161, D.I. 122 at A-8368-69.) The statement does not show that multiple weights were measured for G997 alone. 67. Thus, Ms. Chang’s report is consistent with the sequence of G997 reported in TX 226, which contains a 29 amino acid deletion at the C-terminus relative to the sequence predicted from the gene. (Compare TX 226, D.I. 122 at A-8556.1 with TX 161, D.I. 122 at A-8367, Fig. 1.) 68. Two other sequences were determined by Dr. Jorgensen for alpha-amylas-es produced from the same source as G997, Bacillus stearothermophilus strain ATCC No. 39,709, and those sequences have fewer than 29 amino acids deleted from their C-terminuses. (TX 135, D.I. 122 at A-8357; TX 201, D.I. 122 at A-8531; Jorgensen, Tr. at 661:15-663:7.) However, those sequences were not determined from samples of G997 alpha-amylase as sold by Defendants, and so the sequences do not demonstrate variations in G997. While the sequences reflected in exhibits TX 135 and TX 201 have different C-terminal endings than the sequence in TX 226, those differences apparently reflect variations in conditions of protein expression, including the organism in which the protein is produced. (Jorgensen, Tr. at 663:8-16, 664:9-15.) 69.In sum, the preponderance of the evidence shows that there is one sequence for G997: the one reported in TX 226. I conclude that TX 226 accurately states the sequence of G997. III. CONCLUSIONS OF LAW 1. Jurisdiction over the subject matter of this action is proper under 28 U.S.C. §§ 1331 and 1338. A. Claim Construction 2. A patent infringement analysis involves two steps: claim construction and the application of the construed claim to the accused process or product. Mark-man v. Westview Instruments, Inc., 52 F.3d 967, 976 (Fed.Cir.1995) (en banc), aff'd, 517 U.S. 370, 116 S.Ct. 1384, 134 L.Ed.2d 577 (1996). To allow the trial to be held on an expedited basis, I bifurcated this case and combined the claim construction hearing and liability phase of the trial. (See 10/19/05 preliminary injunction hearing transcript at 65.) 3. Patent claims are construed as a matter of law. Cybor Corp. v. FAS Techs., Inc., 138 F.3d 1448, 1454-56 (Fed.Cir.1998) (en banc). “[T]he words of a claim ‘are generally given their ordinary and customary meaning.’ ” Phillips v. AWH Corp., 415 F.3d 1303, 1312 (Fed.Cir.2005) (en banc) (quoting Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed.Cir.1996)). That ordinary meaning “is the meaning that the term would have to a person of ordinary skill in the art in question at the time of the invention.” Id. at 1313. 4. To determine the ordinary meaning of a term, the court should review “the same resources as would” the person of ordinary skill in the art. Multiform Desicants, Inc. v. Medzam, Ltd., 133 F.3d 1473, 1477 (Fed.Cir.1998). Those resources include “the words of the claims themselves, the remainder of the specification, the prosecution history, and extrinsic evidence concerning relevant scientific principles, the meaning of technical terms, and the state of the art.” Innova/Pure Water, Inc. v. Safari Water Filtration Sys., Inc., 381 F.3d 1111, 1116 (Fed.Cir.2004). 5. “[T]he claims themselves provide substantial guidance as to the meaning of particular claim terms.” Phillips, 415 F.3d at 1314. Both “the context in which a term is used in the asserted claim” and the “[o]ther claims of the patent in question” are useful for understanding the ordinary meaning. Id. 6. “[T]he specification ‘is always highly relevant to the claim construction analysis. Usually, it is dispositive; it is the single best guide to the meaning of a disputed term.’ ” Id. at 1315 (quoting Vitronics, 90 F.3d at 1582). In short, the claims “must be read in view of the specification, of which they are a part.” Markman, 52 F.3d at 979. Thus, “[t]he construction that stays true to the claim language and most naturally aligns with the patent’s description of the invention will be, in the end, the correct construction.” Renishaw PLC v. Marposs Societa’ per Azioni, 158 F.3d 1243, 1250 (Fed.Cir.1998). 7. On occasion, “the specification may reveal a special definition given to a claim term ... that differs from the meaning it would otherwise possess. In such cases, the inventor’s lexicography governs.” Phillips, 415 F.3d at 1316 (citing CCS Fitness, Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed.Cir.2002)). The specification may also “reveal an intentional disclaimer, or disavowal, of claim scope by the inventor ... [which] is regarded as dispositive.” Id. (citing SciMed Life Sys., Inc. v. Advanced Cardiovascular Sys., Inc., 242 F.3d 1337, 1343-44 (Fed.Cir.2001)). 8. The court “should also consider the patent’s prosecution history.” Markman, 52 F.3d at 980. “Like the specification, the prosecution history provides evidence of how the [Patent and Trademark Office] and the inventor understood the patent.” Phillips, 415 F.3d at 1317 (citing Lemelson v. Gen. Mills, Inc., 968 F.2d 1202, 1206 (Fed.Cir.1992)). 9. The court may rely on extrinsic evidence, which is “all evidence external to the patent and prosecution history, including expert and inventor testimony, dictionaries, and learned treatises.” Markman, 52 F.3d at 980. In particular, “dictionaries, and especially technical dictionaries, ... have been properly recognized as among the many tools that can assist the court in determining the meaning of particular terminology.” Phillips, 415 F.3d at 1318 (citing Teleflex, Inc. v. Ficosa N. Am. Corp., 299 F.3d 1313, 1325 (Fed.Cir.2002)). However, extrinsic evidence is “less significant than the intrinsic record in determining ‘the legally operative meaning of claim language.’ ” C.R. Bard, Inc. v. U.S. Surgical Corp., 388 F.3d 858, 862 (Fed.Cir.2004) (quoting Vanderlande Indus. Nederland BV v. Int’l Trade Comm’n, 366 F.3d 1311, 1318 (Fed.Cir.2004)). 10. During claim construction, “[t]he sequence of steps used by the judge in consulting various sources is not important; what matters is for the court to attach the appropriate weight to be assigned to those sources in light of the statutes and policies that inform patent law.” Phillips, 415 F.3d at 1324. 11. Here, the parties agree about the meaning of the terms “variant,” which is used in claims 1, 3, and 5, and “parent,” which is used in claim 1. A variant is a protein that has been derived from a parent protein by protein engineering, so that there are substitutions, insertions, or deletions of amino acids in the variant relative to the parent. (’031 patent, 3:59-67; Arnold, Tr. at 137:23-138:9; Alber, Tr. at 202:8-11.) 12. The parties dispute the meaning of two claim terms: “Bacillus stearothermo-philus alpha-amylase,” which is used in claims 1 and 5, and “% homology,” which is used in claims 1 and 3. 1. “Bacillus stearothermophilus Alpha-Amylase” a. The Parties’ Proposed Constructions 13. Novozymes contends that a Bacilkis stearothermophilus alpha-amylase is “the functional enzyme product that is produced from the alpha-amylase gene of a Bacillus stearothermophilus organism.” (D.I. 118 at 18.) 14.Defendants propose two constructions of the term. First, they argue that the ’031 patent prosecution history shows that the applicants defined Bacillus stear-othermophilus alpha-amylase as “an alpha-amylase having the amino acid sequence of SEQ ID NO:3.” (D.I. 116 at 5.) Alternatively, they argue that a person having ordinary skill in the art would understand that a Bacillus stearothermophilus alpha-amylase is “a 514- or 515-amino acid protein encoded by a wild type Bacillus stear-othermophilus alpha-amylase gene, minus the signal sequence.” (Id. at 8-9.) 15. The parties at least agree with the starting proposition that a Bacillus stear-othermophilus alpha-amylase is produced from a gene taken from a Bacillus stear-othermophilus bacterium. The narrowing constructions proposed by Defendants require that the alpha-amylase have either a particular sequence or a particular length. b. The Court’s Construction 16. I conclude that Novozymes’s construction is the correct one. Neither the prosecution history nor the evidence concerning the expected length of an alpha-amylase supports the adoption of the narrower constructions proposed by Defendants. i. The Term is Not Limited to SEQ ID NO:3 17. Defendants’ argument for their first proposed construction is based on the prosecution history of the ’031 patent, specifically, the applicants’ response to the examiner’s written description and enablement rejections. (D.I. 116 at 5-8.) 18. In the first office action, when the examiner issued rejections for failure to satisfy the written description and enablement requirements, she suggested that the rejections could be overcome by amending the claims to require “at least 80% identity” between the variant and SEQ ID NO:3. (FF ¶ 29.) In their response, the applicants did not make the suggested change, and instead amended the claims to require “at least 80% homology” between the variant and the parent Bacillus stear-othermophilus alpha-amylase. (FF ¶ 37.) In the second office action, the examiner, upon further consideration, again rejected the claims, and suggested that the rejections could be overcome by requiring “at least 90% identity” between the variant and SEQ ID NO:3. (FF ¶ 41.) The applicants responded by canceling the claims and adding new claims that required “at least 95% homology” between the variant and the parent Bacillus stearothermophi-lus alpha-amylase. (FF ¶ 50.) In support of those new claims, the applicants noted the examiner’s suggestion that the variants have 90% homology to SEQ ID NO:3 and argued that the rejection was “rendered moot ... as the new claims recite a homology of 95%.” (Id.) 19.According to Defendants, that exchange demonstrates that the applicants and the examiner both understood that the “Bacillus stearothermophilus alpha-amylase” was the same as “SEQ ID NO:3.” (D.I. 116 at 7-8.) However, the prosecution history establishes that the examiner and the applicants recognized that the terms were not synonymous. In the second office action, the examiner pointed out that the applicants had not adopted her suggestion, but that the amendments were “similar.” (FF ¶ 40.) In their response to the second office action, the applicants stated that their invention was “directed to variants of Bacillus stearothermophilus alpha-amylase enzymes and to alpha-amylase variants having 95% homology to SEQ ID NO:3.” (TX 101, D.I. 121 at A-7736.) The applicants also stated that the specification described “variants of Bacillus stearothermophilus and variants having at least 95% homology to SEQ ID NO:3.” (Id. at A-7735.) Those statements describe two different sets of variants, those defined relative to Bacillus stearothermophi-lus alpha-amylase and those defined relative to SEQ ID NO:3. Thus, contrary to Defendants’ argument (D.I. 116 at 7-8), the record shows that the examiner and applicants understood that “SEQ ID NO:3” was not used interchangeably with “Bacillus stearothermophilus alpha-amylase” or “parent Bacillus stearothermophi-lus alpha-amylase.” That record is also consistent with the claims: claims 1 and 5 refer to a “Bacillus stearothermophilus alpha-amylase,” and claim 3 refers to “SEQ ID NO:3.” (’031 patent, 65:11-17, 65:21-66:12, 66:16-19.) 20. Therefore, the term “Bacillus stearothermophilus alpha-amylase” is not limited to SEQ ID NO:3. ii. The Term is Not Limited to Proteins of a Particular Length 21. Defendants’ argument for their second proposed construction is based on the examples in the ’031 patent and on extrinsic evidence about alpha-amylases. 22. First, Defendants note that the examples of Bacillus stearothermophilus alpha-amylases disclosed in the patent have either 514 or 515 amino acids. (D.I. 116 at 9 (citing ’031 patent, Fig. 1, 7:32-35, sequence listing for SEQ ID NO:3).) 23. Second, Defendants emphasize extrinsic evidence to show that, at the patent’s critical date in 1995, Bacillus stear-othermophilus alpha-amylases would have been expected to have 514 or 515 amino acids after the removal of the N-terminal signal sequences. (Alber, Tr. at 209:2-18, 209:25-210:5, 211:6-212:3, 212:19-214:8; TX 142; TX 568; TX 628; TX 629; TX 630; TX 633; TX 634; TX 635.) According to Defendants, that information means that, by definition, a “Bacillus stearother-mophilus alpha-amylase” must be 514 or 515 amino acids in length. (D.I. 116 at 9-10.) 24. I disagree with Defendants’ conclusion that length is a defining feature of Bacillus stearothermophilus alpha-amylas-es. First, none of the evidence adduced by Defendants reports the complete, experimentally determined amino acid sequence of an alpha-amylase. Instead, that evidence shows the results of DNA sequencing of genes, alone (TX 142; TX 629; TX 630; TX 666) or in combination with amino acid sequencing of the N-terminus of the protein (TX 568; TX 628; TX 634; TX 666), and the results of gel electrophoresis experiments (TX 633; TX 635). That evidence may lead to the expectation that, if one were to do the experiment, an alpha-amylase would have a precise length of 514 or 515 amino acids. However, in 1995 the experiment remained to be done. 25. Second, even if Defendants had shown that all Bacillus stearothermophi-lus alpha-amylases had a specific length— which they have not shown — none of the evidence, including the ’031 patent itself, dictates that a Bacillus stearothermophi-lus alpha-amylase must have a particular length. The fact that examples in the patent have a given length is not sufficient to make that length a defining feature of Bacillus stearothermophilus alpha-amylas-es. I conclude that a person having ordinary skill in the art would not understand the ’031 patent to impose such a length requirement. 26. Therefore, the term “Bacillus stearothermophilus alpha-amylase” is not limited to proteins having 514 or 515 amino acids. 27. Accordingly, I conclude that the construction proposed by Novozymes is correct. A Bacillus stearothermophilus alpha-amylase is “the functional enzyme product that is produced from the alpha-amylase gene of a Bacillus stearothermo-philus organism.” 2. “% Homology ” a. The Parties’ Proposed Constructions 28. Novozymes proposes that “% homology” means “a percent identity calculation according to the standard whereby the number of exactly matching amino acid residues in two sequences is compared to the total number of residue positions that are present in both sequences, expressed as a percent, e.g., as implemented by the GAP GCG program.” (D.I. 118 at 19.) 29. Defendants argue that the calculation of homology “requires use of any method that accounts for all substitutions, insertions, and deletions, including internal and terminal deletions, over the entire amino acid sequences of the variant and parent alpha-amylases identified in the claims.” (D.I. 115 at 63, ¶ 16.) That calculation is not consistent with Novozymes’s proposed construction, primarily because Novozymes’s calculation method does not count deletions. b. The Court’s Construction 30. Because Novozymes’s proposed construction is consistent with unambiguous instructions given in the ’031 patent, I conclude that it is the correct construction. 31. According to the patent: An amino acid sequence is considered to be X % homologous to the parent a-amylase if a comparison of the respective amino acid sequences, performed via known algorithms, such as the one described by Lipman and Pearson in Science 227 (1985) p. 1435, reveals an identity of X %. The GAP computer program from the GCG package, version 7.3 (June 1993), may suitably be used, employing default values for GAP penalties [Genetic Computer Group (1991) Programme Manual for the GCG Package, version 7, 575 Science Drive, Madison, Wis., USA 53711]. (’031 patent, 4:36-45.) Thus, according to that passage, “% homology” is equivalent to percent identity. (Devereux, Tr. at 124:22-25, 128:9-13; Arnold, Tr. at 140:6-14; Alber, Tr. at 294:5-9.) Also, the passage sets forth a methodology that, first, aligns the sequences and, second, calculates the percent identity from the alignment. (Devereux, Tr. at 126:9-12; Arnold, Tr. at 145:14-20; Alber, Tr. at 233:22-24.) Finally, a software package is suggested that “may suitably be used” to perform the alignment and calculation of identity. 32. Novozymes’s construction is based on the methodology used by that software package. In the GAP program, identity is calculated by counting the number of exact matches of amino acid residues between two aligned sequences and dividing by the number of positions where there are residues present in both sequences. (Devereux, Tr. at 109:22-110:6.) When one sequence has a residue with no corresponding residue in the other sequence, the program allows a gap in the alignment, and that position is not counted in the denominator of the identity calculation. (Id. at 109:13-21,110:7-111:12.) 33. Defendants argue that even though the patent states that GAP is suitable for the calculation, a person having ordinary skill in the art would understand that using GAP would be incorrect. (D.I. 116 at 11-14.) First, Defendants note that while GAP “may suitably be used,” it is not required, and that other methods for doing the calculation were available when the specification was written, methods that might give a different result. (Id. at 11-12 (citing Arnold, Tr. at 181:12-182:10, 190:19-191:3; Alber, Tr. at 234:25-235:8).) 34. Second, Defendants argue (D.I. 116 at 13-14) that the ’031 specification teaches that deletions, which will cause gaps in an alignment, are important modifications that can be made by protein engineers. Indeed, the patent includes deletions in its general description of possible modifications (’031 patent, 3:59-65) and the claims themselves require deletions at positions 179 and 180 (id., 65:11-17, 65:21-66:12, 66:16-19). In addition, Defendants cite extrinsic evidence to support the proposition that a person having ordinary skill in the art would understand that deletions were important in the field of protein engineering. (TX 511, D.I. 122 at A-8886, ¶ 30; Alber, Tr. at 216:9-217:6, 217:20-218:20.) Because of that importance, Defendants contend, those skilled in the art would know that deletions should be included in the calculation of percent identity. 35. While I agree that the ’031 patent discloses that deletions are relevant modifications, those general statements, which are not made in the context of a discussion of percent identity, are not sufficient to overcome the express instruction that GAP may suitably be used. Indeed, the presence of both the commentary on deletions and the instruction regarding GAP shows that the patentee gave the instructions with full understanding about the importance of deletions. It was no oversight or mistake. While the patent does not instruct that GAP is the only way to do the calculation, that does not imply, as Defendants suggest, that GAP should not be used. A construction that requires that GAP not be used would be contrary to the express language of the patent. 36. I conclude that t