1. Sequence Search and Analysis Christopher.low@uspto.gov SPE 1653 (703) 308-2923

2. Biosequence Patent Search Mission Impossible - ? Mission Difficult - ?

3. Sample Searchable Public Databases National Center for Biotechnology Information (NCBI) Entrez –www.ncbi.nlm.nih.gov European Bioinformatics Institute (EBI) –www.ebi.ac.uk DNA DataBank of Japan (DDBJ) –www.ddbj.nig.ac.jp SwissProt, PIR, etc do not cover patents

4. NCBI Entrez NCBI Genbank –In collaboration with EMBL and DDBJ Databases from other producers –SwissProt, TrEMBL, PDB, PIR, etc Bibliographic databases –E.g., PubMed (MEDLINE) NCBI BLAST ® sequence searching

5. EMBL-EBI on the Web EMBL databases –EMBL Nucleotide Database (i.e. GenBank) –Translated EMBL (TrEMBL) Databases from other producers –SwissProt, PDB, etc Many sequence search options: FASTA, NCBI-BLAST, WU-Blast, Smith-Waterman

6. DDBJ via the Web DDBJ databases –DNA DataBank of Japan (i.e. GenBank) –Protein Mutant Database (PMD) Databases from other producers –Protein Databank (PDB) Several sequence search options: FASTA, BLAST, Smith-Waterman

7. USPTO Nucleic Acid Databases –GenEmbl (GenBank) –N-Genseq –ESTs Protein Databases –Protein Databank (PDB) –SwissProt –A-Genseq

8. Searched Sequence HIV protease PQITLWQAPLVTIKIGGQLKEALLDT GADDTVLEEMNLPGRWKPKMIGGIG GFIKVAQYDQILIEICGHKAIGTVLVG PTPVNIIGANLLTQIGCT Default parameters selected

9. Searched Sequence – Results - A Database: Protein sequences derived from the Patent division of GenBank 78 Hits |gb|AAN27487.1| Sequence 17 from patent US 6440730 Length = 1003 Score = 191 bits (486), Expect = 4e-50 Identities = 93/96 (96%), Positives = 93/96 (96%) |gb|AAN27487.1| Query1 : PQITLWQAPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVAQYD 60 PQITLWQ PLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKV QYD PQITLWQ PLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKV QYD Sbjct: 57 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVGQYD 116 Query1 : QILIEICGHKAIGTVLVGPTPVNIIGANLLTQIGCT 96 QILIEICGHKAIGTVLVGPTPVNIIG NLLTQIGCT QILIEICGHKAIGTVLVGPTPVNIIG NLLTQIGCT Sbjct: 117 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCT 152

10. Searched Sequence – Results - B Database: Protein Data Base (PDB) 75 Hits gi|230577|pdb|2HVP| HIV-1 Protease Length = 99 Score = 172 bits (437), Expect = 1e-44 Identities = 93/96 (96%), Positives = 93/96 (96%) gi|230577|pdb|2HVP| gi|230577|pdb|2HVP| Query1 : PQITLWQAPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVAQYD 60 PQITLWQ PLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKV QYD PQITLWQ PLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKV QYD Sbjct: 57 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD 60 Query1 : QILIEICGHKAIGTVLVGPTPVNIIGANLLTQIGCT 96 QILIEICGHKAIGTVLVGPTPVNIIG NLLTQIGCT QILIEICGHKAIGTVLVGPTPVNIIG NLLTQIGCT Sbjct: 117 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCT 96

11. Searched Sequence – Results - C Title: TITLE OF YOUR APPLICATION GOES HERE Perfect score: 521 Sequence: 1 PQITLWQRPLVTIKIGGQLK..........TPVNIIGRNLLTQIGCTLNF 99 Scoring table: BLOSUM62 Gapop 10.0, Gapext 0.5 Searched: 908470 seqs, 133250620 residues Total number of hits satisfying chosen parameters: 908470 Minimum DB seq length: 0 Maximum DB seq length: 2000000000 Post-processing: Minimum Match 0% Maximum Match 100% Listing first 45 summaries Database : A_Geneseq_101002:*

12. Searched Sequence – Results - D RESULT 1 ID AAU77767 standard; Protein; 99 AA. AC AAU77767; DT 05-JUN-2002 (first entry) DE Human immunodeficiency virus type 1 (HIV-1) related protein #1. KW Human immunodeficiency virus type 1; HIV-1; protease. OS Unidentified. PN KR98066681-A. PD 15-OCT-1998. PF 28-JAN-1997; 97KR-0002361. PR 28-JAN-1997; 97KR-0002361. PA (GLDS ) LG CHEM LTD. PI Kwon YD, Lee TG; DR WPI; 1999-598487/51. PT Mutated human immunodeficiency virus type 1 (HIV-1) protease PT and process for preparing the same - PS Example 3; Page 10; 18pp; Korean. CC The invention relates to a mutated human immunodeficiency CC virus type 1 (HIV-1) protease and a process for preparing the CC mutants. This sequence represents a human immunodeficiency CC virus associated protein described in the invention. SQ Sequence 99 AA;

13. Searched Sequence – Results - E Pred. No. is the number of results predicted by chance to have a score greater than or equal to the score of the result being printed, and is derived by analysis of the total score distribution. SUMMARIES % Result Query No. Score Match Length DB ID Description ------------------------------------------------------------- 1 521 100.0 99 20 AAU77767 Human immunodefici 15 516 99.0 177 11 AAR05744 HIV-1 protease gen SQ Sequence 99 AA; RESULT 1 Query Match 100.0%; Score 521; DB 20; Length 99; Query Match 100.0%; Score 521; DB 20; Length 99; Best Local Similarity 100.0%; Pred. No. 2.6e-58; Best Local Similarity 100.0%; Pred. No. 2.6e-58; Matches 99; Conservative 0; Mismatches 0; Indels 0; Gaps 0; Matches 99; Conservative 0; Mismatches 0; Indels 0; Gaps 0; Qy 1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Db 1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD 60 Qy 61 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99 ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| Db 61 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99

14. Searched Sequence – Results - F Pred. No. is the number of results predicted by chance to have a score greater than or equal to the score of the result being printed, and is derived by analysis of the total score distribution. SUMMARIES % Result Query No. Score Match Length DB ID Description ------------------------------------------------------------- 1 521 100.0 99 20 AAU77767 Human immunodefici 15 516 99.0 177 11 AAR05744 HIV-1 protease gen SQ Sequence 177 AA; RESULT 15 Query Match 99.0%; Score 516; DB 11; Length 177; Query Match 99.0%; Score 516; DB 11; Length 177; Best Local Similarity 99.0%; Pred. No. 2.3e-57; Best Local Similarity 99.0%; Pred. No. 2.3e-57; Matches 98; Conservative 1; Mismatches 0; Indels 0; Gaps 0; Matches 98; Conservative 1; Mismatches 0; Indels 0; Gaps 0; Qy 1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD 60 ||||||||||||||||||||||||||||||||||||:||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||:||||||||||||||||||||||| Db 56 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD 115 Qy 61 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99 ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| Db 116 QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 154

15. Sample Claims A polypeptide having HIV protease activity An isolated polypeptide having HIV protease activity An isolated polypeptide comprising SEQ ID NO: 1 An isolated polypeptide consisting essentially of SEQ ID NO: 1 An isolated polypeptide consisting of SEQ ID NO: 1 A peptide fragment having HIV protease activity A peptide fragment of SEQ ID NO: 1 with HIV protease activity A epitope of ten amino acids in length of SEQ ID NO: 1 capable of binding to an antibody to SEQ ID NO:1 An isolated polypeptide or fragment thereof of SEQ ID NO: 1 wherein one or more of amino acid residues have been substituted, deleted, or inserted and which polypeptide retains HIV protease enzymatic activity

16. Acknowledgements STIC / Toby Port and David Schreiber TC 1600 / James Martinell