General

Branden, C., and J. Tooze. 1999. Introduction to Protein Structure, 2nd ed. New York: Garland Publishing, Inc. This is a classic, and the illustrations are very helpful.

Primary Structure

Doolittle, J., J. Abelson, and M. Simon, eds. 2009. Molecular Evolution: Computer Analysis and Nucleic Acid Sequences. Methods in Enzymology, vol. 183 (Amsterdam: Elsevier). A collection of articles on computational analysis of DNA and protein sequences and the construction of phylogenetic trees.

Wolf, M.Y., Y.I. Wolf, and E.V. Koonin. 2008. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol. Direct 3:40–55. A comprehensive resource for comparison of protein sequences and how they relate to evolution.

Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357–366. This report is widely considered to be the founding paper in the field of molecular evolution.

Secondary Structure

Ramachandran, G.N., C. Ramakrishnan, and V. Sasisekharan. 1963. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95–99.

Rost, B. 2001. Review: Protein secondary structure prediction continues to rise. J. Struct. Biol. 134:204–218.

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Tertiary and Quaternary Structures

de Juan, D., F. Pazos, and A. Valencia. 2013. Emerging methods in protein co-evolution. Nat. Rev. Genet. 14:249–261.

Koonin, E.V., R.L. Tatusov, and M.Y. Galperin. 1998. Beyond complete genomes: From sequence to structure and function. Curr. Opin. Struct. Biol. 8:212–217. A review on accuracy in the correlation of sequences with function in genomics.

Ponting, C.P., and R.R. Russell. 2002. The natural history of protein domains. Annu. Rev. Biophys. Biomol. Struct. 31:45–71. A description of how structural databases can be used to study evolution.

Protein Folding

Dill, K.A., and J.L. MacCallum. 2012. The protein-folding problem, 50 years on. Science 338:1042–1046.

Jackson, W.S., A.W. Borkowski, N.E. Watson, O.D. King, H. Faas, A. Jasanoff, and S. Lindquist. 2013. Profoundly different prion diseases in knock-in mice carrying single PrP codon substitutions associated with human diseases. Proc. Natl. Acad. Sci. USA, doi: 10.1073/pnas.1312006110.

Khatib, F., F. DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, S. Cooper, M. Kazmierczyk, M. Gilski, S. Krzywda, H. Zábranská, I. Pichová, et al. 2011. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat. Struct. Mol. Biol. 18:1175–1177.

Koloday, R., D. Petrev, and B. Honig. 2006. Protein structure comparison: Implications of the nature of “fold space,” and structure and function prediction. Curr. Opin. Struct. Biol. 16:393–398.

Determining the Atomic Structure of Proteins

Cavanagh, J., W. Fairbrother, A. Palmer, and A. Skelton. 2007. Protein NMR Spectroscopy: Principles and Practice, 2nd ed. San Diego: Academic Press.

Rhodes, G. 2006. Crystallography Made Crystal Clear: A Guide to Users of Molecular Models, 3rd ed. San Diego: Academic Press.