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Lesk: Introduction to Bioinformatics: 3e
Chapter 06
Protein folding
Baldwin, R.L. and Rose, G.D. (1999). Is protein folding hierarchic? I. Local structure and peptide folding. II. Folding intermediates and transition states. Trends in Biochemical Science 24, 26-32; 77-83. [DOI: 10.1016/S0968-0004(98)01345-0]
Rose, G.D., Fleming, P.J., Banavar, J.R. and Maritan, A. (2006). A backbone-based theory of protein folding. Proceedings of the National Academy of Sciences, USA, 103, 16623-16633. Discussions of current thinking about protein stability and folding. [DOI: 10.1073/pnas.0606843103]
Structure alignment and sequence-structure relationships
Holm. and Sander, C. (1995). Dali: a network tool for protein structure comparison. Trends in Biochemical Science, 20, 478-480. Describes DALI and its applications to structural alignment.
Connections among sequences, structures and functions.
Das, R., Junker, J., Greenbaum, D. and Gerstein, M.B. (2001). Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond. The Pharmacogenomics Journal, 1, 115-125.
Galperin, M.Y. and Koonin, E.V. (2003). Sequence-Evolution-Function/Computational Approaches in Comparative Genomics. Kluwer Publishers, Boston, MA.
State of the art in homology modelling and its application in structural genomics.
Guex, N., Diemand, A. and Peitsch, M.C. (1999). Protein modelling for all. Trends in Biochemical Science, 24, 364-367; Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research, 31, 3381-3385. Descriptions of SWISS-MODEL.
Peitsch, M.C., Schwede, T. and Guex, N. (2000). Automated protein modelling-the proteome in 3D. Pharmacogenomics, 1, 257-266. What it will take to complete the structural genomics problem. [DOI: 10.1517/14622416.1.3.257]
Martí-Renom, M.A., Stuart, A.C., Fiser, A., Sánchez, R., Melo, F. and Šali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291-325. [DOI: 10.1146/annurev.biophys.29.1.291]
Pieper, U., Eswar, N., Braberg, H., Madhusudhan, M.S., Davis, F.P., Stuart, A.C., Mirkovic, N., Rossi, A., Marti-Renom, M.A., Fiser, A., Webb, B., Greenblatt, D., Huang, C.C., Ferrin, T.E. and Šali, A. (2004). MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research, 32, D217-D222. [PubMed: 14681398] [DOI: 10.1093/nar/gkh095]
Tramontano, A. (2004). Integral and differential form of the protein folding problem. Physics of Life Reviews, 1, 103-127. [DOI: 10.1016/j.plrev.2004.05.002]
Tramontano, A. (2006). Protein Structure Prediction: Concepts and Applications. Wiley-VCH Verlag, Weinheim, Baden-Württemberg, Germany.
Other protein structure prediction methods
Bonneau, R. and Baker, D. (2001). Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure, 30, 173-189. Recent review of structure prediction methods by authors of the most successful of them. [PubMed: 11340057] [DOI: 10.1146/annurev.biophys.30.1.173]
Structure-based drug discovery
Abraham, D.J. (2007). Structure-based drug design-a historical perspective and the future. In: Comprehensive Medicinal Chemistry II. Mason, J.S., volume. Mason, J.S., volume edited by; Triggle, D. and Taylor, J.edited by; eds. in chief. Vol. 4, 1-22. Elsevier, Amsterdam.
Introduction to molecular visualization
Lesk, A.M., Bernstein, H.J. and Bernstein, F.C. (2008). Molecular graphics in structural biology. In: Computational Structural Biology. Peitsch, M. and Schwede, T., eds. World Scientific Publishing.
Classics still well worth reading
Kauzmann, W. (1959). Some factors in the interpretation of protein denaturation. Advances in Protein Chemistry, 14, 1-63. [PubMed: 14404936]
Richards, F.M. (1977). Areas, volumes, packing and protein structure. Annual Review of Biophysics and Bioengineering, 6, 151-176. [PubMed: 326146] [DOI: 10.1146/annurev.bb.06.060177.001055]
Chothia, C. (1984). Principles that determine the structure of proteins. Annual Review of Biochemistry, 53, 537-572. [PubMed: 6383199] [DOI: 10.1146/annurev.bi.53.070184.002541]
Richards, F.M. (1991). The protein folding problem. Scientific American 264 (1), 54-57; 60-63.