Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2007-02-12
2010-06-29
Brusca, John S (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000
Reexamination Certificate
active
07747393
ABSTRACT:
The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.
REFERENCES:
patent: 6537776 (2003-03-01), Short
patent: 6605449 (2003-08-01), Short
patent: 7315786 (2008-01-01), Dahiyat et al.
patent: 2001/0051855 (2001-12-01), Wang et al.
patent: 2002/0045175 (2002-04-01), Wang et al.
patent: 2002/0048772 (2002-04-01), Dahiyat et al.
patent: 2002/0155460 (2002-10-01), Schellenberger et al.
patent: 2003/0032059 (2003-02-01), Wang et al.
patent: 2004/0072245 (2004-04-01), Gustafsson et al.
patent: 2004/0161796 (2004-08-01), Gustafsson et al.
patent: 2005/0084907 (2005-04-01), Fox
patent: 2006/0205003 (2006-09-01), Gustafsson et al.
patent: 2008/0132416 (2008-06-01), Fox
patent: 2008/0133143 (2008-06-01), Gustafsson et al.
patent: 2008/0147369 (2008-06-01), Fox
patent: 2008/0220990 (2008-09-01), Fox
patent: WO01/59066 (2001-08-01), None
patent: WO01/61344 (2001-08-01), None
patent: WO03/055978 (2003-07-01), None
patent: WO03/075129 (2003-08-01), None
patent: WO2006/002267 (2006-01-01), None
Berglund et al., “INLR, Implicit Non-Linear Latent Variable Regression,” J. of Chemometrics, vol. 11, pp. 141-156 (1997)).
Hellberg et al., “The Prediction of Bradykinin Potentiating Potency of Pentapeptides. An Example of a Peptide Quantitative Structure-Activity Relationship,” Acia Chemica Scandinaviea B 40, pp. 135-140, 1988.
Bucht et al., “Optimising the Signal Peptide for Glycosyl Phosphatidylinositol Modification of Human Acetylcholinesterase Using Mutational Analysis and Peptide-Quantitative Structure-Activity Relationships,” Biochimica et Biophysica Acta 1431, pp. 471-482, 1999.
Sandberg et al., “Engineering Multiple Properties of a Protein by Combinatorial Mutagenesis,” Proc. Natl. Acad. Sci. USA, vol. 90, pp. 8367-8371, Sep. 1993.
Wrede et al., “Peptide Design Aided by Neural Networks: Biological Activity of Artificial Signal Peptidase I Cleavage Sites,” Biochemistry, 37, pp. 3588-3593, 1998.
Sandberg et al., “New Chemical Descriptors Relevant for the Design of Biologically Active Peptides. A Multivariate Characterization of 87 Amino Acids,” J. Med Chem., 41, pp. 2481-2491, 1998.
Casari et al., “A Method to Predict Functional Residues in Proteins,” Nat. Struct Biol., 2, pp. 171-178, 1995.
Suzuki et al., “A Method for Detecting Positive Selection at Single Amino Acid Sites,” Mol. Biol. Evol. 16 (10): pp. 1315-1328, 1999.
Benner et al., “Amino Acid Substitution During Functionally Constrained Divergent Evolution of Protein Sequences,” Protein Engineering, vol. 7, No. 11, pp. 1323-1332, 1994.
Wu et al., “Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families,” Proc. Int. Conf. Intell. Syst. Mol. Biol., 4, pp. 230-240, 1996.
Adenot et al., “Peptides Quantitative Structure-Function Relationships: An Automated Mutation Strategy to Design Peptides and Pseudopeptides from Substitution Matrices,” Journal of Molecular Graphics and Modelling, 17, pp. 292-309, 1999.
Norinder et al., “A Quantitative Structure-Activity Relationship Study of Some Substance P-Related Peptides,” J. Peptide Res., 49, pp. 155-162, 1997.
Sandberg, “Deciphering Sequence Data a Multivariate Approach,” Ph.D Thesis, Umea: Umea University, 78 pages, 1997.
Eriksson et al., “Peptide QSAR on Substance P Analogues, Enkephalins and Bradykinins Containing L-and D-Amino Acids,” Acta Chemica Scandinavica, 44, pp. 50-56, 1990.
Ufkes eta l., “Further Studies on the Structure-Activity Relationships of Bradykinin-Potentiating Peptides,” European Journal of Pharmacology, 79, pp. 155-158, 1982.
Dobrynin et al., “Synthesis of Model Promoter for Gene Expression inEscherichia coli,” Symposium Series No. 7, pp. 365-376, 1980.
Skinner et al., “Potential Use of Additivity of Mutational Effects in Simplifying Protein Engineering,” Proc. Natl. Acad. Sci., vol. 93, pp. 10753-10757, 1996.
Lathrop et al., “Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Score Functions,” J. Mol. Biol., 255, pp. 641-665, 1996.
Hellberg et al., “A Multivariate Approach to QSAR,” Ph.D. Thesis, Umea, Sweden: University of Umea: 1986.
Nambier et al., “Total Synthesis and Cloning of a Gene Coding for the Ribonuclease S Protein,” Science, 223: 1299-1301, 1984.
Lin et al., “Functional Expression of Horseradish Peroxidase inE. coliby Directed Evolution,” Biotechnol. Prog, 15: 467-471, 1999.
Lathrop R.H., “The Protein Threading Problems with Sequence Amino Acids Interaction Preference is NP-Complete,” Protein Eng., 7:1059-1068, 1994.
Hanes et al., “In Vitro Selection and Evolution of Functional Proteins by Using Ribosomes Display,” Proc. Natl. Acad. Sci. USA, 94: 4937-4942, 1997.
Wells et al., “Rapid Evolution of Peptide and Protein Binding Properties in vitro,” Curr Opin Biotechnol, 3:355-362, 1992.
Johnson et al., “The Traveling Salesman Problem: A Case Study in Local Optimization,” In Local Search in Combinatorial Optimization, Edited by Aarts et al., John Wiley & Sons Ltd., 21-310, 1997.
Jonsson et al., “Quantitative Sequence-Activity Models (QSAM)—Tools for Sequence Design,” Nucleic Acids Res., 21:733-739, 1993.
Geladi et al., “Partial Least Squares Regression: A Tutorial,” Anal Chim Acta, 168: 1-17, 1986.
Holowachuk et al., “Efficient Gene Synthesis by Klenow Assembly/Extension-Pfu Polymerase Amplification (KAPPA) of Overlapping Olingonucleotides,” PCR Methods Appl, 4:299-302, 1995.
Hellberg et al., “Minimum Analogue Peptide Sets (MAPS) for Quantitative Structure-Activity Relationships,” Int J Pept Protein Res, 37:414-424, 1991.
Mee et al., “Design of Active Analogues of a 15-Residue Peptide Using D-Optimal Design, QSAR and a Combinatorial Search Algorithm,” J Pept Res, 49:89-102, 1997.
Schneider et al., “Peptide Design by Artificial Neural Networks and Compouter-Based Evolutionary Search,” Proc Natl Acad Sci USA, 95:12179-12184, 1998.
Sjostrom et al.,“Signal Peptide Amino Acid Sequences inEscharichla coliContain Information Related to Final Protein Localization, A Multivariate Data Analysis,” EMBO, 6:823-891, 1987.
Patel et al., “Patenting Computer-Designed Peptides,” Journal of Computer-Aided Molecular Design, 12:543-556, 1998.
Aita et al., “Theory of Evolutionary Molecular Engineering Through Simultaneous Accumulation of Advantageous Mutations,” J. Theor. Biol., 207:543-556, 2000.
Darius et al., “Simulated Molecular Evolution of Computer Generated Artifacts?,” Biophysical Journal, 67:2120-2122, 1994.
Singh et al., “Application of Genetic Algorithms to Combinatorial Synthesis: A Computational Approach to Lead Identification and Lead Optimization,” J.Am. Chem. Soc., 118:1669-1676, 1996.
Aita et al., “Analysis of Local Fitness Landscape with a Model of the Rough Mt. Fuji-Type Landscape: Application to Prolyl Endopeptidase and Thermolysin,” Biopolymers. vol. 54, pp. 64-79, Accepted Jan. 14, 2000.
Gogos et al., “Assignment of Enzyme Substrate Specificity by Principal Component Analysis of Aligned Protein Sequences: An Experimental Test Using DNA Glycosylase Homologs,” Proteins: Structure, Function, and Genetics, 40, pp. 98-105, 2000.
Vector NTI Suite 7.0 User's Manual (po
Brusca John S
Kruse Norman J.
Maxygen Inc.
Skibinsky Anna
Weaver Austin Villeneuve & Sampson LLP
LandOfFree
Methods, systems, and software for identifying functional... 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, systems, and software for identifying functional..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods, systems, and software for identifying functional... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4155344