Computational Molecular Biology

Discrete Protein Sequence Motifs

Doug Brutlag

November 4, 2008

Bairoch, A., Bucher, P. and Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucleic Acids Res, 25(1), 217-21.

Bairoch, A. and Apweiler, R. (1997). The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res, 25(1), 31-6.

Barton, G. J. 1990. Protein multiple sequence alignment and flexible pattern matching. Meth Enzymol 183:403&endash;427.]

Bork, P. 1989. Recognition of functional regions in primary structures using a set of property patterns. Febs Letters 257:191&endash;195.

Bork, P., & Gibson, T. J. (1996). Applying motif and profile searches. Methods Enzymol, 266, 162-84.

Bork, P., & Koonin, E. V. (1996). Protein Sequence Motifs. Current Opinion in Structural Biology, 6(3), 366-376.

Brazma, A. et al. (1998). Approaches to the automatic discovery of patterns in biosequences. J Comput Biol, 5(2), 279-305.

Brazma, A. et al. (1996). Discovering patterns and subfamilies in biosequences. Ismb, 4, 34-43.

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Grundy, W. N., Bailey, T. L. and Elkan, C. P. (1996). ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput Appl Biosci, 12(4), 303-310.

Grundy, W. N. et al. (1997). Meta-MEME: motif-based hidden Markov models of protein families. Comput Appl Biosci, 13(4), 397-406.

Henikoff, S. And Henikoff, J.G. (1991) "Automated assembly of protein blocks for database searching" Nucleic Acids Res., 19, 6565&endash;6572.

Henikoff, S., Greene, E. A., Pietrokovski, s., Bork, P., Attwood, T. K. and Hood, L. (1997). Gene Families: The taxonomy of protein paralogs and chimeras. Science, 278(24 October 1997), 609-614.

Jimenez-Montano, M. A., and Zamora-Cortina, L. 1981. Evolutionary model for the generation of amino acid sequences and its application to the study of mammal alpha-hemoglobin chains. In Proceedings of the Seventh International Biophysics Congress, Mexico City.

Kidera, A., Yonishi, Y., Masahito, O., Ooi, T., and Scheraga, H. A. 1985. Statistical analysis of the physical properties of the twenty naturally occurring amino acids. J Prot Chem 4:23&endash;55.

Livingstone, C. D., & Barton, G. J. (1996). Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol, 266, 497-512.

Miyata, T., Miyazawa, S., and Yasunaga, T. 1979. Two types of amino acid substitution in protein evolution. J Mol Evol 12:219&endash;236.

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Mocz, G. 1995. Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins. Protein Sci 4:1178&endash;1187.

Moore, J. F., Engelberg, A., & Bairoch, A. (1988). Using PC/Gene for protein and nucleic acid analysis. Biotechniques, 6, 566-572.

Patthy, L. (1987). Detecting homology of distantly related proteins with consensus sequences. J. Mol. Biol., 198, 567-577.

Patthy, L. (1996). Consensus Approaches in Detection of Distant Homologies. Methods in Enzymology, 266, 184-197.

Poch, O., & Delarue, M. (1996). Converting Sequence Block Alignments into Structural Insights. Methods in Enzymology, 266, 662-680.

Posfai, J., Bhagwat, A. S., Posfai, G. and Roberts, R. J. (1989). Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 17 (7), 2421-35.

Sander, C. and Schneider, R. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics 9:56&endash;68.

Saqi, M. A. S. and Sternberg, M. J. E. (1994). Identification of sequence motifs from a set of proteins with related function. Protein Engineering 7 (2), 165-171.

Saqi, M. A. and Sayle, R. (1994). PdbMotif--a tool for the automatic identification and display of motifs in protein structures. Comput Appl Biosci, 10(5), 545-6.

Smith, H. O., Annau, T. M. and Chandrasegaran, S. (1990). Finding sequence motifs in groups of functionally related proteins. Proc Natl Acad Sci U S A, 87(2), 826-30.

Staden, R. (1988). Methods to define and locate patterns of motifs in sequences. Comput Appl Biosci, 4 (1), 53-60.

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Smith, R. F. and Smith, T. F. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci USA 87:118&endash;122, 1990.

Taylor, W. R. The classification of amino acid conservation. J Theor Biol 119:205&endash;218, 1986.

Tatusov, R. L., Altschul, S. F. and Koonin, E. V. (1994). Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A 91 (25), 12091-5.

Tatusov, R. L., Koonin, E. V. and Lipman, D. J. (1997). A Genomic Perspective of Protein Families. Science, 278(24 October), 631.

Taylor, W. R. (1986). Identification of protein sequence homology by consensus template alignment. J. Mol. Biol., 188, 233-258.

Thornton, J. M. and Gardner, S. P. (1989). Protein motifs and data-base searching. Trends Biochem Sci, 14 (7), 300-4.

Wu, T. D., and Brutlag, D. L. 1995. Identification of protein motifs using conserved amino acid properties and partitioning techniques. ISMB&endash;95, pages 402&endash;410.

Wu, T. D., & Brutlag, D. L. (1996). Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families. ISMB-96, 3, 230-240.

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