Recommended Readings Fasman, G.D. (ed.) "Prediction of Protein Structure and the Principles of Protein Conformation". New York (Plenum), 1989. The most comprehensive treatise on protein structure prediction available. Filled with dozens of contributions and reviews from many of the foremost experts in the field. An excellent introduction to the subject. Highly recommended for both novice and expert alike. Doolittle, R.F. (ed.) "Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences". Methods in Enzymology, Vol. 183, 1990. A fine complement to Fasman's work. This is an equally comprehensive review with in depth descriptions and useful assessments of numerous sequence analysis algorithms and programs. Provides good summaries of how the field has developed and where the field is likely to go. An excellent source-book for methods and ideas for sequence alignment, sequence assessment and cladistic deconvolution. Doolittle, R.F. "Of URFs and ORFs: A Primer of How to Analyze Derived Amino Acid Sequences". California (University Science Books), 1987 A gem of a book. One of the easiest to understand "how-to" references you can find. Among the most informative texts on the subject of protein sequence analysis. Get it before it goes out of print. Schulz, G.E. A Critical Evaluation of Methods for Prediction of Protein Secondary Structures, Ann. Rev. Biophys. and Biophys. Chem. 17, 1-22 (1988). A very fair-minded critique of secondary structure prediction methods. Offers a quick and easy-to-read introduction to the potential applications and probable short-comings of protein structure prediction. Taylor, W.R. Pattern Matching Methods in Protein Sequence Comparison and Structure Prediction, Protein Eng. 2, 77-86 (1988). An extremely informative review of the field as it stood in 1988. Well written and easy to read. Offers some excellent insights into a number of newer (and older) methods or algorithms. Highly recommended. General References Altschul, S.F., Gish, W., Miller, W., Myers, E.W., & Lipman, D.J. Basic Local Alignment Search Tool, J. Mol. Biol. 215, 403-410 (1990). Barton, G.J. & Sternberg, M.J.E. A Strategy for the Rapid Multiple Alignment of Protein Sequences, J. Mol. Biol. 198, 327-337 (1987). Chou, P.Y. & Fasman, G.D. Empirical Predictions of Protein Conformation, Ann. Rev. Biochem. 47, 251-276 (1978). Chou, P.Y. & Fasman, G.D. Prediction of Protein Conformation, Biochemistry 13, 222-245 (1974). Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. & DeLisi, C. Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic Structure in Proteins, J. Mol. Biol. 195, 659-685 (1987). Creighton, T.E. Proteins: Structures and Molecular Properties, W.H. Freeman, New York (1984). Dayhoff, M.O., Barker, W.C. & Hunt, L.T. Establishing Homologies in Protein Sequences, Methods in Enzymology 91, 524-545 (1983) Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. A Model of Evolutionary Change in Proteins, Atlas of Protein Structure 5 (Suppl. 3) 345-352 (1979). Eisenberg, D., Weiss, R.M. & Terwilliger, R.C. The Hydrophobic Moment Detects Periodicity in Protein Hydrophobicity, Proc. Nat. Acad. Sci. (USA) 81, 140-144 (1984). Fasman, G.D. & Gilbert, W.A. The Prediction of Transmembrane Protein Sequences and Their Conformation: an Evaluation, TIBS 15, 89-92 (1990) Garnier, J., Ogusthorpe, D.J. & Robson, B. Analysis of the Accuracy and Implementation of Simple Methods for Predicting the Secondary Structure of Globular Proteins, J. Mol. Biol. 120, 97-120 (1978). Gibrat, J.F., Garnier, J. & Robson, B. Further Development of Protein Secondary Structure Prediction Using Information Theory, J. Mol. Biol. 198, 425-443 (1987). Gribskov, M., McLachlan, A.D. & Eisenberg, D. Profile Analysis: Detection of Distantly Related Proteins, Proc. Nat. Acad. Sci. (USA) 84, 4355-4358 (1987). Karplus, P.A. & Schulz, G.E. Prediction of Chain Flexibility in Proteins, Naturewissenschaften 72, 212-213 (1985). Klein, P., Kanehisa, M. & DeLisi, C. The Detection and Classification of Membrane-Spanning Proteins, Biochim. Biophys. Acta 815, 468-476. Kyte, J. & Doolittle, R.F. A New Hydrophobicity Scale, J. Mol. Biol. 157, 105-132 (1982). Lesk, A.M., Levitt, M. & Chothia, C. Alignment of the Amino Acid Sequences of Distantly Related Proteins Using Variable Gap Penalties, Protein Eng. 1, 77-78 (1986). Levin, J.M. & Garnier, J. Improvements in a Secondary Structure Method Based on a Search for Local Sequence Homologies and its use as a Model Building Tool, Biochim. Biophys. Acta 955, 283-295 (1988). Levin, J.M., Robson, B. & Garnier, J. An Algorithm for Secondary Structure Determination in Proteins Based on Sequence Similarity, FEBS Lett. 205, 303-308 (1986). Lipman, D.J. & Pearson, W.R. Rapid and Sensitive Protein Similarity Searches, Science, 227, 1435-1441 (1985). McLachlan, A.D. Tests for Comparing Related Amino-acid Sequences: Cytochrome C & Cytochrome C551, J. Mol. Biol. 61, 409-423 (1971). Needleman, S.B. & Wunsch, C.D. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins, J. Mol. Biol. 48, 443-453 (1970). Nishikawa, K. & Ooi, T. Amino Acid Sequence Homology Applied to Protein Secondary Structures and Joint Prediction with Existing Methods, Biochim. Biophys. Acta 871, 45-54 (1986). Parker, J.M.R., Guo, D., & Hodges, R.S. New Hydrophobicity Scale Derived from HPLC Peptide Retention Data, Biochemistry 25, 5425-5431 (1986). Pearson, W.R. & Lipman D.J. Improved Tools for Biological Sequence Comparison, Proc. Nat. Acad. Sci. (USA) 85, 2444-2448 (1988). Richards, F.M. Areas, Volumes, Packing and Protein Structure, Ann. Rev. Biophys. Bioeng. 6, 151-175 (1977). Rooman, M.J. & Wodak, S.F. Identification of Predictive Sequence Motifs Limited by Protein Structure Database Size, Nature 335, 45-49 (1988). Rooman, M.J. & Wodak, S.J. Weak Correlation Between Predictive Power of Individual Sequence Patterns and Overall Prediction Accuracy in Proteins, Proteins: Struct. Func. Gen. 9, 68-78 (1991). Rooman, M.J., Rodriguez, J. & Wodak, S.J. Relations Between Protein Sequence and Structure and Their Significance, J. Mol. Biol. 213, 337-350 (1990). Schwartz, R.M. & Dayhoff, M.O. Matrices for Detecting Distant Relationships, Atlas of Protein Structure 5 (Suppl. 3) 353-358 (1979). Sweet, R.M. Evolutionary Similarity Among Peptide Segments is a Basis for Predicting Protein Folding, Biopolymers 25, 1566-1577 (1986). Williams, R.W., Chang, A., Juretic, D., Loughram, S. Secondary Structure Predictions and Medium Range Interactions, Biochim. Biophys. Acta 916, 200-204 (1987).