Advanced Molecular Biology

March 8, 2000

Structure from Sequence

Doug Brutlag

Barton, G. J. (1995). Protein secondary structure prediction. Curr. Opin. Struct. Biol., 5, 372-376.

Berger, B., Wilson, D. B., Wolf, E., Tonchev, T., Milla, M., & Kim, P. S. (1995). Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. USA, 92, 8259-8263.

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol., 112, 535-542.

Chou, P. Y., & Fasman, U. D. (1974). Prediction of protein conformation. Biochemistry, 13, 211-215.

Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., & Fletterick, R. J. (1986). Turn prediction in proteins using a pattern-matching approach. Biochemistry, 25, 266-275.

Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B., & Mornon, J.-P. (1993). Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng., 6(4), 377-382.

Di Francesco, V., Garnier, J., & Munson, P. J. (1996). Improving protein secondary structure prediction with aligned homologous sequences. Protein Science, 5, 106-113.

Di Francesco, V., Munson, P. J., & Garnier, J. (1995, ). Use of multiple alignments in protein secondary structure prediction. Paper presented at the Twenty-eighth annual Hawaii international conference on system sciences.

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Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure prediction. Proteins: Struct. Funct. Genet., 23, 566-579.

Frishman, D., & Argos, P. (1996). Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng., 9(2), 133-142.

Frishman, D., & Argos, P. (1997). Seventy-five percent accuracy in protein secondary structure prediction. Proteins: Struct. Funct. Genet., 27, 329-335.

Garnier, J., Gibrat, J.-F., & Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol, 266, 540-553.

Garnier, J., Osguthorpe, D. J., & Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol., 120, 97-120.

Heringa, J., Sommerfeldt, H., Higgins, D., & Argos, P. (1992). OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. CABIOS, 8(6), 599-600.

Holley, H. L., & Karplus, M. (1989). Protein secondary structure prediction with a neural network. Proc. Natl. Acad. Sci. USA, 86, 152-156.

Hubbard, T. J., & Park, J. (1995). Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials. Proteins: Struct. Funct. Genet., 23, 398-402.

Hubbard, T. J. P. (1994, ). Use of beta-strand interaction pseudo-potentials in protein structure prediction and modeling. Paper presented at the Biotechnology Computing Track, 27th HICSS.

Jones, D. T., Taylor, W. R., & Thornton, J. M. (1994). A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 33, 3038-3049.

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Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.

Kidera, A., Konishi, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J. Protein Chem., 4(1), 23-55.

King, R. D., & Sternberg, M. J. E. (1996). Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Science, 5, 2298-2310.

Klingler, T. M., & Brutlag, D. L. (1994). Discovering structural correlations in alpha-helices. Protein Science, 3, 1847-1857.

Krogh, A., & Riis, S. K. (1996, ). Prediction of beta sheets in proteins. Paper presented at the Advances in neural information processing systems 8.

Lifson, S., & Sander, C. (1980). Specific recognition in the tertiary structure of beta-sheets of proteins. J. Mol. Biol., 139, 627-639.

Lim, V. I. (1974). Algorithms for prediction of alpha-helical and beta- structural regions in globular proteins. J. Mol. Biol., 88, 875-894.

Matthews, B. W. (1975). Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.

Mehta, P. K., Heringa, J., & Argos, P. (1995). A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Science, 4, 2517-2525.

Munson, P. J., Di Francesco, V., & Porrelli, R. (1993, ). Secondary structure prediction using penalized likelihood models. Paper presented at the 25th Symposium on the Interface, Computing Science and Statistics, San Diego, California.

Munson, P. J., Di Francesco, V., & Porrelli, R. (1994, ). Protein secondary structure prediction using periodic-quadratic-logistic models: Statistical and theoretical issues. Paper presented at the Twenty-seventh annual Hawaii international conference on system sciences.

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Nishikawa, K. (1983). Assessment of secondary-structure prediction of proteins - comparison of computerized Chou-Fasman methods with others. Biochim. Biophys. Acta., 748, 285-299.

Presnell, S. R., Cohen, B. I., & Cohen, F. E. (1992). A segment-based approach to protein secondary structure prediction. Biochemistry, 31, 983-993.

Qian, N., & Sejnowski, T. J. (1988). Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol., 202, 865-884.

Riis, S. K., & Krogh, A. (1996). Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. J. Comp. Biol., 3(1), 163-183.

Rost, B., Casadio, R., Fariselli, P., & Sander, C. (1995). Transmembrane helices predicted at 95% accuracy. Protein Science, 4, 521-533.

Rost, B., Fariselli, P., & Casadio, R. (1996). Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science, 5, 1704-1718.

Rost, B., & Sander, C. (1993). Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.

Rost, B., & Sander, C. (1994). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct. Funct. Genet., 19, 55-72.

Rost, B., Sander, C., & Schneider, R. (1994). Redefining the goals of protein secondary structure prediction. J. Mol. Biol., 235, 13-26.

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Salamov, A. A., & Solovyev, V. V. (1995). Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J. Mol. Biol., 247, 11-15.