Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2008-09-09
2008-09-09
Clow, Lori A (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000
Reexamination Certificate
active
10817530
ABSTRACT:
A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.
REFERENCES:
patent: 5845049 (1998-12-01), Wu
patent: 5878373 (1999-03-01), Cohen et al.
patent: 6512981 (2003-01-01), Eisenberg et al.
Altschul et al., “Grapped BLAST and PSI-BLAST: a new generation of protein database search programs,”Nucleic Acids Res, 1997;25(17):3389-3402.
Bairoch et al., “The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000,”Nucleic Acids Res, 2000;28(1):45-48.
Ben-Hur et al., “Remote homology detection: a motif based approach,”Bioinformatics, 2003;19(Suppl. 1):i26-i33.
Benner et al., “Amino acid substitution during functionally constrained divergent evolution of protein sequences,”Protein Eng., 1994;7:1323-1332.
“BLAST.” [online]. NCBI Blast.National Institute of Health. [retrieved on Jul. 6, 2004].Retrieved from the Internet:<http:www.ncbi.nlm.nih.gov/BLAST/>;1 pg.
Bowie et al., “A method to identify protein sequences that fold into a known three-dimensional structure,”Science, 1991;253:164-170.
Brenner et al., “The ASTRAL compendium for protein structure and sequence analysis,”Nucleic Acids Res., 2000;28:254-256.
Chandonia et al., “ASTRAL compendium enhancements,”Nucleic Acids Res., 2002;30(1):260-263.
Chothia et al., “The relation between the divergence of sequence and structure in proteins,”EMBO J, 1986;5: 823-826.
“ClustalW.” [online]. European Bioinformatics Institute (EMBL-EBI).[retrieved on Jul. 6, 2004]. Retrieved from the Internet:<http://www.ebi.ac.uk/clustalw/>;2 pgs.
Dubchak et al., “Recognition of a protein fold in the context of the SCOP classification,”Proteins, 1999;35:401-407.
Eddy, S.R., “Profile hidden Markov models,”Bioinformatics, 1998;14:755-763.
“Emotif Maker.” [online]. Biochemistry. Standford University, Standford, CA [retrieved on Jul. 6, 2004].Retrieved from the Internet:<http://fold.stanford.edu/emotif/emotif-maker.html>;2 pgs.
Falquet et al., “The Prosite database, its status in 2002,”Nucleic Acids Res, 2002;30:235-238.
Gough et al., “SuperFamily: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments,”Nucleic Acids Res, 2002;30: 268-272.
Gribskov et al., “Identification of sequence patterns with profile analysis,”Methods Enzymol, 1996;266:198-212.
Henikoff et al., “Increased coverage of protein families with the Blocks Database servers,”Nuclic Acids Res, 2000;28:228-230.
Henikoff et al., “Blocks+: a non-redundant database of protein alignment bloicks derived from multiple compilations,”Bioinformatics, 1999, 15:471-479.
Henikoff et al., “Protein family classification based on searching a database of blocks,”Genomics, 1994;19:97-107.
Higgins et al., “Multiple sequence alignment,”Methods Mol Biol., 2000;143: 1-18.
Holm et al., “Mapping the protein universe,”Science, 2000;273:595-602.
Kelley et al., “Enhanced genome annotation using structural profiles in the program 3D-PSSM,”J Mol Biol, 2000;299: 499-520.
Kostich et al., “Human members of the eukaryotic protein kinase family,”Genome Biol, 2002;3:43.
Kullback et al., “On information sufficiency,”Ann Math Stat, 1951;22: 79-86.
Lo Conte et al., “SCOP database in 2002: refinements accommodates structural genomics,”Nucleic Acids Res, 2002;30: 264-267.
Marcotte et al., “A combined algorithm for genome-wide prediction of protein function,”Nature, 1999;402:83-86.
Marcotte, E.M., “Computational genetics: finding protein function by nonhomology methods,”Curr Opin. Struct. Biol., 2000;10:359-365.
Martelli et al., “A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins,”Bioinformatics, 2002;18: S46-53.
Mathura et al., “Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to DNase I related endonucleases,”Bioinformatics, 2003;19(11):1381-1390.
Mathura et al., “Automated Generation of Property Based Motifs to Search for Functional Neighbors and to Improve Sequence Alignments,”5thMeeting on the Critical Assessment of Techniques for Protein Structure Prediction, CASP5, Asilomar Conference Center, Pacific Grove, CA, Dec. 1-5, 2002: A-178-179.
Mathura et al., “Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to APE,”2002 Bioinformatics Symposium, Rice University, Houston, TX, Oct. 14-15, 2002: 37.
Mathura et al., “Defining Physical-chemical Properties based motifs specific for members of the APE family of DNA repair proteins,”7thStructural Biology Symposium, UTMB, Galveston, TX, May 17-19, 2002:93.
Mathura et al., “Sequence and Structural Analysis of APE 1 Protein Family Using Physical-chemical Properties Based Motifs,”RECOMB, Currents in Computational Moelecular Biology 2002, Washington, DC.: 191-192.
Mathura et al., “Physical-chemical properties based motifs for annotating protein sequences from genomic data,”Molecular Genomics 2002: Profiling of Gene Expression, UTMB, Galveston, TX, Apr. 5-7, 2002:35.
Mathura et al., “Quantitative Descriptors for Amino Acids Based on Physico-Chemical Properties using Vector Representation,”Keck 2000 Symposium, Baylor College of Medicine and Rice University, Houston, TX, Oct. 16-17, 2000: 33.
Mathura et al., “A New Vector Representation of Amino Acids Based on Large Number of Physico-Chemical Properties,”Fifth Annual Structural Biology Symposium, UTMB, Galveston, TX, May 19-21, 2000: 54.
Mehta et al., “Recognizing very distant sequence relationships among proteins by family profile analysis,”Proteins, 1999;35:387-400.
Nagano et al., “One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions,”J Mol Biol, 2002;321:741-765.
Norin et al., “Structural proteomics: developments in structure-to-function predictions,”Trends Biotechnol., 2002;20:79-84.
Overbeek et al., “The use of gene clusters to infer functional coupling,”Proc Natl Acad Sci USA, Mar. 16, 1999;96(6):2896-2901.
Oezguen et al., “APE1: Identifing Motifs by MASIA and Metalion Position by MD-Simulations,”Keck Center 2001 Annual Research Conference, Galveston, TX, Sep. 21, 2001:35.
Press et al., “Numerical Recipes in C: The Art of Scientific Computing,” 1999, Cambridge University Press, New York.
“Prosite Database of protein families and domains.”[online]. Expasy Prosite.[retrieved on Jul. 6, 2004]. Retrieved from the Internet.<http://us.expasy.org/prosite/>;2 pgs.
Rigoutsos et al., “Dictionary-driven protein annotation,”Nucleic Acids Res, 2002;30:3901-3916.
Rison et al., “Comparison of funcitonal annotation schemes for genomes,”Funct Integr. Genomics, 2000;1:56-69.
Rychlewski et al., “Comparison of sequence profiles. Strategies for Structural predictions using sequence information,”Protein Sci, 2000;9:232-241.
Schaffer et al., “IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices,”Bioinformatics, 1999;16:1000-1011.
Schaffer et al., “Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements,”Nucleic Acids Res, 2000;29:2994-3005.
Schein et al., “Total sequence decomposition distinguishes functional modules, &#
Braun Werner
Mathura Venkatarajan S.
Schein Catherine H.
Board of Regents , The University of Texas System
Clow Lori A
Mueting Raasch & Gebhardt, P.A.
LandOfFree
Physical-chemical property based sequence motifs and methods... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Physical-chemical property based sequence motifs and methods..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Physical-chemical property based sequence motifs and methods... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3959006