This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Baker, D., Sali, A. (2001) Protein Structure Prediction and Structural Genomics. Science 294: 93–96.
Baldi, P., Chauvin, Y., Hunkapiller, T., McClure, M. (1994) Hidden Markov models of biological primary sequence information. In: Proc. Natl. Acad. Sci. USA 91: 1059–1063.
Bates, P.A., Sternberg, M.J.E. (1999) Model building by comparison at CASP3: using expert knowledge and computer automation, Proteins: Structure, Function and Genetics. Suppl 3: 47–54.
Batzoglou, S., Pachter, L., Mesirov, J.P., Berger, B., Lander, E.S. (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. Genome Research 10: 950–958.
Berman, H.M., Westbrook, J. Feng, Z. Gilliland, G. Bhat, TN., Weissig, H., Shindyalov, I.N., Bourne, P.E. (2000) The Protein Data Bank, Nucleic Acids Research 28: 235–242.
Contreras-Moreira, B., Bates, P.A. (2002) Domain Fishing: a first step in protein comparative modeling. Bioinformatics 18: 1141–1142.
Friedman, N., Linial, M., Nachman, I., Pe'er, D. (2000) Using Bayesian Network to Analyze Expression Data. Journal of Computational Biology 7: 601–620.
Havel, T.F. and Snow, M.E. (1991) A new method for building protein conformations from sequence alignments with homologues of known structure. J. Mol. Biol. 217: 1–7
Hunter, L. (February 2004) Lecture 17: Computing with Expression Array Results. http://compbio.uchsc.edu/Hunter_lab/Hunter/bioi7711/lecture17.ppt.
Karchin, R. (1999) Hidden Markov Models and Protein Sequence Analysis. In: Proc. 7th International Conference on Intelligent Systems for Molecular Biology.
Kemp, G. (February 2004) Bioinformatics III Lecture: Comparative Modeling. http://www. cs. chalmers.se/~kemp/teaching/bioinformaticsIII/2004/lecture2.pdf.
Kent, W.J. and Zahler, A.M. (2000) Conservation, Regulation, Synteny, and Introns in a Large-scale C. briggsae-C. elegans Genomic Alignment. Genome Research 10: 1115–1125.
Kolinski, A., Betancourt, M.R., Kihara, D., Rotkiewicz, P. and Skolnick, J. (2001) Generalized Comparative Modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins: Structure, Function and Genetics 44: 133–149.
Krogh, A. (1998) An Introduction to Hidden Markov Models for Biological Sequences. In: Computational Methods in Molecular Biology, pp 45–63.
Levitt, M. (1992) Accurate Modeling of Protein Conformation by Automatic Segment Matching. J. Mol. Biol. 226: 507–533.
Purdue, E. (2000) Comparative Genomics. http://www.biospace.com/articles/genomics_comparative.cfm, July.
Ravichandran, S. (November 2003) Homology Modeling: Concepts and Protocols. http://ncisgi.ncifcrf.gov/~ravichas/HomMod/Dec03HomMod.htm.
Richon, A.B. (2001) An Introduction to Molecular Modeling. Mathematech 1: 83.
Rivas, E., Eddy, S.R. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 16: 573–585.
Sali, A. and Blundell, T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779–815.
Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E. and Lancet, D. (2003) GeneNote: whole genome expression profiles in normal human tissues. Comptes Rendus Biologies 326: 1067–1072.
Shmulevich, I., Dougherty, E.R., Kim, S., Zhang, W. (2002) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261–274.
Sjolander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, S.I. and Haussler, D. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Computer Applications in the Biosciences 12: 327–345.
Suter-Crazzolara, C. and Kurapkat, G, (2001) Comparative Genomics for the Mining of Data. Genetic Engineering News 21 11: 34–35.
Tatusov, R.L., Koonin, E.V. and Lipman, D.J. (1997) A Genomic Perspective on Protein Families. Science 278: 631–637.
UCSC, Computational Biology Group (February 2004) Sequence Alignment and Modeling System. http://www.cse.ucsc.edu/research/compbio/sam.html
Varfolomeev, S.D., Uporov, I.V. and Fedorov, E.V. (2002) Bioinformatics and Molecular Modeling in Chemical Enzymology. Active Sites of Hydrolases. Biochemistry (Moscow) 67: 1099–1108.
Velculescu, V.E., Zhang, L., Vogelstein B, Kinzler KW (1995) Serial Analysis of Gene Expression. Science 270: 484–487.
Washington University (December 2003) The Rfam database of RNA alignments and CMs. http://rfam.wustl.edu/
Westhead, D.R. (February 2004) Structural Bioinformatics. http://bbsrcbioinf.leeds.ac.uk/b/structure/lecture2.ppt.
Zapp, M.A. (2002) The Structures of Life. National Institute of General Medical Sciences, http://www.nigms.nih.gov/news/science_ed/structlife.pdf.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Hiedelberg
About this chapter
Cite this chapter
Mann, S., Chen, YP.P. (2005). Modeling for Bioinformatics. In: Chen, YP.P. (eds) Bioinformatics Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26888-X_9
Download citation
DOI: https://doi.org/10.1007/3-540-26888-X_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20873-0
Online ISBN: 978-3-540-26888-8
eBook Packages: Computer ScienceComputer Science (R0)