Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Chemical
Reexamination Certificate
2002-11-01
2011-10-04
Zeman, Mary K (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Simulating nonelectrical device or system
Chemical
C702S019000, C702S020000, C703S011000, C435S006120, C536S024100
Reexamination Certificate
active
08032347
ABSTRACT:
Apparatus, methods, media, signals and data structures for protein sequence analysis are disclosed. A method includes identifying, from among a first group of aligned protein sequences having at least a threshold degree of alignment with a first protein sequence, a second group of at least one of the aligned sequences having at least one insertion or deletion (“indel”) relative to the first protein sequence satisfying a predefined condition. The apparatus may include a processor circuit configured to carry out the method.
REFERENCES:
patent: 6018102 (2000-01-01), Garbarino et al.
patent: 6107316 (2000-08-01), Young et al.
patent: 6127524 (2000-10-01), Casipit et al.
patent: 6168928 (2001-01-01), Read et al.
patent: 6268160 (2001-07-01), Clough et al.
patent: 6306663 (2001-10-01), Kenten et al.
patent: 6358692 (2002-03-01), Jindal et al.
patent: 6541008 (2003-04-01), Wise et al.
patent: 6645747 (2003-11-01), Hallahan et al.
patent: 7572589 (2009-08-01), Reiner et al.
patent: 2003/0158672 (2003-08-01), Ramnarayan et al.
patent: 2010/0151590 (2010-06-01), Reiner et al.
patent: 11318460 (1999-11-01), None
patent: WO 97/01578 (1997-01-01), None
Higgins et al. (Methods in Enzymology vol. 266, pp. 383-402, 1996).
Mott et al. Journal of Comuptational Biology vol. 6 No. 1, 1999.
Taylor, WR. J Mol. Biol. 1997 269:902-943.
Storey et al. J computational Biol. vol. 8 No. 5, 2001 p. 549-556.
Hein et al. J Mol. Biol. 200 302:265-279.
Aebischer, T., et al. Proteophosphoglycan, a major secreted product of intracellular Leishmania mexicana amastigotes, is a poor B-cell antigen and does not elicit a specific conventional CD4′ T-cell response. Infect Immun (1999) 67(10):5379-5385.
Altschul, S.F., et al. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs. Nucleic Acids Res. (1997) 25(17):3389-3402.
Andersen, G.R., et al. Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Bα complex. Nat Struct Biol (2001) 8:531:534.
Aronov, A.M., et al. Rational design of selective submicromolar inhibitors of tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase. Biochemistry (2000) 39(18):4684-91.
Bairoch, A. and Apweiler R. The SWISS-PROT protein sequence database: its relevance to human molecular medical research. J Mol Med (1997) 75(5):312-316.
Bairoch, A. and Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acid Res (2000) 28(1):45-48.
Baldauf, S.L., et al. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. PNAS (1993) 90:11558-62.
Baldwin, G.C., et al. Human immunodeficiency virus causes mononuclear phagocyte dysfunction. Proc Nati Acad Sci USA (1990) 87:3933-3937.
Barral, A., et al. Transforming growth factor β as a virulence mechanism forLeishmania braziliensis. Proc Natl Acad Sci USA (1993) 90:3442-3446.
Basu, N., et al. Down-regulation of mannose receptors on macrophages after infection withLeishmania donovani. Biochem J (1991) 277 (Pt 2):451-456.
Beatty, W.L., et al. Identification of mycobacterial surface proteins released into subcellular compartments of infected macrophages. Infect Immun (2000)68(12):6997-7002.
Berg, K.L. et al. The major SHP-1-binding, tyrosine-phosphorylated protein in macrophages is a member of the KIR/LIR family and an SHP-1 substrate. Oncogene (1998) 17:2535-2541.
Beverley, S.M. Hijacking the cell: parasites in the driver's seat. Cell (1996) 87(5):787-789.
Binstadt, B.A., et al. SLP-76 is a direct substrate of SHP-1 recruited to killer cell inhibitory receptors. J Biol Chem (1998) 273(42):27518-27523.
Blanchette, J., et al. Leishmania-induced increases in activation of macrophage SHP-1 tyrosine phosphatase are associated with impaired IFN-γ-triggered JAK2 activation. Eur J Immunol (1999) 29:3737-3744.
Blasioli, J., et al. Definition of the sites of interaction between the protein tyrosine phosphatase SHP-1 and CD22*. J Biol Chem (1999) 274(4):2303-2307.
Blery, M., et al. Early signaling via inhibitory and activating NK receptors. Hum Immunol (2000) 61:51-64.
Bliska, J.B., et al. Signal transduction in the mammalian cell during bacterial attachment and entry. Cell (1993) 73(5):903-920.
Bonafonte, M.T., et al. Isolation of the gene coding for elongation factor-1alpha inCryptosporidium parvum. Biochim Blophys Acta (1997) 1351(3):256-60.
Borges, M.M., et al. Potent stimulation of the innate Immune system by aLeishmania brasillensisrecombinant protein. Infect Immun (2001) 69(9):5270-7.
Bouchard, P., et al. Phosphorylation and Identification of a major tyrosine phosphorylation site in protein tyrosine phosphatase 1C*. J Biol Chem (1994) 269(30):19585-19589.
Bousquet, C., et al. sst2 somatostatin receptor mediates negative regulation of insulin receptor signaling through the tyrosine phosphatase SHP-1*. J Biol Chem (1998) 273(12):7099-7106.
Brummel, J.H., et al. Regulation of Src homology 2-containing tyrosine phosphatase 1 during activation of human neutrophlls. J Biol Chem (1997) 272(2):875-882.
Button, L.L., et al. RecombinantLeishmaniasurface glycoprotein GP63 is secreted in thebaculovirusexpression system as a latent metalloproteinase. Gene (1993) 134(1):75-81.
Carrero, J.C., et al. Cloning and characterization of Entamoeba histolytica antigens recognized by human secretory IgA antibodies. Parisitol Res (2000) 86(4):330-4.
Chan, J., et al. Lipoarabinomannan, a possible virulence factor involved in persistence of Mycobacterium tuberculosis within macrophages. Infect Immun (1991) 59(5):1755-1761.
Chen, H.E. , et al. Regulation of colony-stimulating factor 1 receptor signaling by the SH2 domain-containing tyrosine phosphatase SHPTP1. Mol Cell Biol (1996) 16(7):3685-3897.
Ciechanover, A., et al. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays (2000) 22:442-451.
Clayton, C., et al. Protein trafficking in kinetoptastid protozoa. Microbiol Rev (1995) 59(3):325-344.
Clough, B., et al. Antibiotic inhibitors of organellar protein synthesis inPlasmodium falciparum. Protist (1999) 159(2):189-95.
Coggeshall, K.M. Negative signaling in health and disease. Immunol Res (1999) 19(1):47-64.
Cohen, G.B., et al. Modular binding domains in signal transduction proteins. Cell (1995) 80(2):237-248.
Colonna, M., et al. A novel family of Ig-like receptors of HLA class I molecules that modulate function of lymphoid and myeloid cells. J Leukoc Biol (1999) 68(3):375-381.
Condeelis, J. Elongation factor 1α, translation and the cytoskeleton. Trends Biochem Sci (1995) 20:169-170.
Damen, J.E., et al. Phosphorylation of tyrosine 503 in the erythropoietin receptor (EpR) is essential for binding the P85 subunit of phosphatidylinositol OPI) 3-kinase and for EpR-associated Pi 3-kinase activity. J Biol Chem (1995) 270:23402-23408.
Darnell, J.E., Jr., et al. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science (1994) 264(5164):1415-1421.
David, M., et al. Differential regulation of the alpha/beta interferon-stimulated Jak/Stat pathway by the SH2 domain-containing tyrosine phosphatase SHPTP1. Mol Cell Biol (1995) 15(12):7050-7058.
David, M., et al. The SH2 domain-containing tyrosine phosphatase PTP1D is required for interferon α/β gene expression. J Biol Chem (1996) 271(27)15862-15865.
Dell, K.R., et al. Stage-specific regulation of protein phosphorylation inLeishmania major. Mol Biochem Parasitol (1994) 64(2):283-292.
Denny, P.W., et al. Acylation-dependent protein export inLeishmania. J Biol Chem (2000) 275(15):11017-11025.
Descoteaux, A., et al. c-fos and tumor necrosis factor gene expression inLeishmania donovani-infected macrophages. Mol and Cell Biol (1989) 9(11):5223-5227.
Deshaies, R.J. SCF and Cullin/Ring H2-based ubiquitin ligases. Annual Review in Cellular Development Biology (1999) 15:435-467.
Dong, Q., et al. Negative regulation of myeloid cell proliferation and function by the SH2 domain-containing tyrosine phosphatase-11. J Immunol (1999) 162:3220-3230.
Dustin, L.B., et al. Expression
Nandan Devki
Reiner Neil E.
Tcherkassov Artem
Bozicevic, Filed & Francis LLP
Francis Carol L.
The University of British Columbia
Zeman Mary K
LandOfFree
Methods and apparatus for protein sequence analysis does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods and apparatus for protein sequence analysis, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods and apparatus for protein sequence analysis will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4256327