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Appendix A: Recommended reading

A.A Protein Structure

J-P. Doucet. Computer-aided molecular design: theory and Applications. Academic Press Harcourt brace & Company, Publishers (ISBN 0-12-221285-1).

Protein Structure Prediction: A practical Approach. Edited by Michael J.E. Sternberg. Oxford University Press (ISBN 0 19 9634973).

The Protein Folding Problem and Tertiary Structure Prediction. Edited by Kenneth M Merz, Jr and Scott M. Le Grand. Bikhäuser Verlag. (ISBN 3-7643-3693-5).

C. Branden and J. Tooze. Introduction to Protein Structure. Garland, New York (1991).

A.V. Efimov. A novel super-secondary structure of proteins and the relation between the structure and amino acid sequence. FEBS Lett. 166, 33-38 (1984).

A.V. Efimov. Structure of a-a-hairpins with short connections. Protein Engin.4, 245-250 (1991).

A.V. Efimov. Structure of b-b-hairpins and b-b-corners. FEBS Lett., 284, 288-292 (1991).

R.H. Kretsinger. Structure and evolution of calcium modulated proteins. CRC Crit. Rev. Biochem. 8, 119-174 (1980).

D.H. Ohlendorf, W.F. Anderson, M. Lewis, C.O. Pabo and B.W. Matthews. Comparison of the structures of cro and lambda repressor proteins in bacteriophage lambda. J. Mol. Biol. 169 757-769 (1983).

B.L. Sibanda, T.L. Blundell and J.M. Thornton. Conformation of b-hairpins in protein structures. J.Mol. Biol. 206, 759-777 (1989).

B.L. Sibanda and J.M. Thornton. B-hairpin families in globular proteins. Nature 316, 170-174 (1985).

C. Chothia, M. Levitt and D. Richardson. Structure of proteins: Packing of a helices and b sheets. Proc. Natl. Acad. Sci. USA74 4130-4134 (1977).

C. Chothia. Principles that determine the structure of proteins. Ann. Rev. Biochem. 53 537-572 (1984).

A.M. Lesk. Protein architecture: a practical approach. IRL press, Oxford (1991).

S.T. Rao and M.G. Rossman. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76 241-256 (1973).

J.S. Richardson. The anatomy and taxonomy of protein structure Adv. Prot. Chem. 34 167-339 (1981).

A.B Protein modelling

Schwede, T.; Sali, A.; Eswar, N.; Peitsch, M.C. Protein Structure Modeling, in: Schwede, T.; Peitsch, M.C. (Ed.). (2008). Computational structural biology, Singapore: World Scientific , S. 700.

S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman. Basic local alignment search tool. J. Mol. Biol. 215:403-410 (1990).

J. Bajorath, R. Stenkamp, A. Aruffo Knowledge-based model building of proteins: Concepts and examples. Prot. Sci. 2:1798-1810 (1993).

B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, M. Karplus CHARMM: A program for macromolecular energy, minimization and dynamics calculation. J. Comp. Chem. 4:187-217 (1983).

C. Chothia, A.M. Lesk. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826 (1986).

Guex, N. and Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723. (1997)

Guex N, Diemand A and Peitsch M. C.  Protein modelling for all. TiBS 24:364-367 (1999)

Guex N, Schwede T and Peitsch M. C.  Protein tertiary structure modelling.  Current Protocols in Protein Science. Unit 2.8: 2.8.1-2.8.17 (1999).

X. Huang, M. Miller. A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12:337-357 (1991).

R. Lüthy, J.U. Bowie, D. Eisenberg. Assessment of protein models with three-dimensional profiles. Nature 356:83-85 (1992).

W.R. Pearson, D.J. Lipman. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85:2444-2448 (1988).

M.C. Peitsch Protein modelling by E-Mail. Bio/Technology (Nature) 13:658-660 (1995).

M.C. Peitsch. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24:274-279 (1996).

Sippl, J.M. (1990) Calculation of Conformational Ensembles from Potentials of Mean Force: an approach to the knowledge based prediction of local structures in globular proteins. J. Mol. Biol. 213,859-883 (1990).

M.J. Sippl. Recognition of errors in three-dimensional structres of proteins. Proteins Struct. Funct. Genet. 17:355-362 (1993).

A.C Hybrid Structure Determination

Integrative/Hybrid examples at PDB dev