References

Altschul et al., 1990

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

Barton, 1993

Barton, G. J. (1993). An efficient algorithm to locate all locally optimal alignments. Comp. App. Biosci. 9, 729-734.

Barton, 1995

Barton, G. J. (1995). Protein secondary structure prediction. Current Opinion Structural Biol. 5, 372-376.

Barton &Sternberg, 1990

Barton, G. J. &Sternberg, M. J. E. (1990). Flexible protein sequence patterns - a sensitive method to detect weak structural similarities. J. Mol. Biol. 212, 389-402.

Bazan, 1990

Bazan, J. F. (1990). Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Nat. Acad. Sci. 87, 6934-6938.

Benner et al., 1993

Benner, S. A., Badcoe, I., Cohen, M. A. &Gerloff, D. L. (1993). Predicted secondary structure for the src homology 3 domain. J. Mol. Biol. 229, 295-305.

Benner et al., 1994

Benner, S. A., Gerloff, D. L. &Jenny, T. F. (1994). Predicting protein crystal structures. Science, 265, 1642-1644.

Bernstein et al., 1977

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanovichi, T. &Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.

Bork, 1995

Bork, P. Margolis, B. (1995). A phosphotyrosine interaction domain. Cell, 80, 693-694.

Bowie &Eisenberg, 1993

Bowie, J. U. &Eisenberg, D. (1993). Inverted protein structure prediction. Current Opinion Structural Biol. 3, 437-444.

Brannigan et al., 1995

Brannigan, J. A., Dodson, G., Duggleby, H. J., Moody, P. C. E., Smith, J. L., Tomchick, D. R. &Murzin, A. G. (1995). A protein catalytic framework with and N-terminal nucleophile is capable of self-activation. Nature, 378, 416-419.

Chothia, 1992

Chothia, C. (1992). One thousand families for the molecular biologist. Nature, 357, 543-544.

Clark et al., 1991

Clark, D. A., Shirazi, J. &Rawlings, C. J. (1991). Protein topology prediction through constraint-based search and the evaluation of topological folding rules. Prot. Eng. 4, 751-760.

Cohen et al., 1986

Cohen, F. E., Kosen, P. A., Kuntz, I. D., Epstein, L. B., Ciardelli, T. L. &Smith, K. A. (1986). Structure-activity studies of interleukin-2. Science, 234, 349-352.

Cohen &Sternberg, 1980

Cohen, F. E. &Sternberg, M. J. E. (1980). On the use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J. Mol. Biol. 137, 9-22.

Cohen et al., 1980

Cohen, F. E., Sternberg, M. J. E. &Taylor, W. R. (1980). Analysis and prediction of protein beta-sheet structures by a combinatorial approach. Nature, 285, 378-382.

Cohen et al., 1982

Cohen, F. E., Sternberg, M. J. E. &Taylor, W. R. (1982). The analysis and prediction of the tertiary structure of globular proteins involving the packing of helices against a sheet: a combinatorial appraoch. J. Mol. Biol. 156, 821-862.

Crawford et al., 1987

Crawford, I. P., Niermann, T. &Kirschner, K. (1987). Predictions of secondary structure by evolutionary comparison: application to the subunit of tryptophan synthase. Proteins, 1, 118-129.

Curtis et al., 1991

Curtis, B. M., Presnell, S. R., Srinivasan, S., Sassenfeld, H., Klinke, R., Jeffery, E., Cosman, D., March, C. J. &Cohen, F. E. (1991). Experimental and theoretical studies of the three-dimensional structure of human interleukin-4. Proteins, 11, 111-119.

Edwards &Perkins, 1995

Edwards, Y. J. K. &Perkins, S. J. (1995). The protein fold of the von willebrand factor type A is predicted to be similar to the open twisted -sheet flanked by -helices found in human ras-p21. FEBS Letters, 358, 283-286.

Gerloff et al., 1995

Gerloff, D. L., Chelvanayagam, G. &Benner, S. A. (1995). A predicted consensus structure for the protein-kinase c2 homology (c2h) domain, the repeating unit of synaptotagmin. Proteins, 22, 299-310.

Gribskov et al., 1987

Gribskov, M., McLachlan, A. D. &Eisenberg, D. (1987). Profile analysis: Detection of distantly related proteins. Proc. Nat. Acad. Sci. 84, 4355-4358.

Holm &C., 1995

Holm, L. &C., S. (1995). 3-d lookup: fast protein structure database searches at 90 %reliability. Proc. 3rd Int. Conf. Intel. Sys. Mol. Biol. , 179-187.

Holm &Sander, 1994a

Holm, L. &Sander, C. (1994a). Searching protein structure databases has come of age. Proteins, 19, 165-173.

Holm &Sander, 1994b

Holm, L. &Sander, C. (1994b). Parser for protein folding units. Proteins, 19, 256-268.

Huang et al., 1994

Huang, Z., Gabriel, J., Baldwin, M. A., Fletterick, R. J., Prusiner, S. B. &Cohen, F. E. (1994). Proposed three-dimensional structure for the cellular prion protein. Proc. Nat. Acad. Sci. 91, 7139-7143.

Hurle et al., 1987

Hurle, M. R., Matthews, C. R., Cohen, F. E., Kuntz, I. D., Toumadje, A. &Johnson, W. C. (1987). Prediction of the tertiary structure of the -subunit of tryptophan synthase. Proteins, 2, 221-224.

Islam et al., 1995

Islam, S. A., Luo, J. C. &Sternberg, M. J. E. (1995). Identification and analysis of domains in proteins. Prot. Eng. 8, 513-525.

Jin et al., 1994

Jin, L., Cohen, F. E. &Wells, J. A. (1994). Structure from function: screening structural models with functional data. Proc. Nat. Acad. Sci. 91, 113-117.

Jones &Thornton, 1993

Jones, D. &Thornton, J. (1993). Protein fold recognition. J. Comp. Aid. Mol. Des. 7, 439-456.

Jones et al., 1992

Jones, D. T., Taylor, W. R. &Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.

Kabsch &Sander, 1983

Kabsch, W. &Sander, C. (1983). A dictionary of protein secondary structure. Biopolymers, 22, 2577-2637.

Lee et al., 1995

Lee, J., Rieu, P., Arnaout, M. A. &Liddington, R. (1995). Crystal structure of the A domain from the subunit of integrin CR3 (CD11b/CD18). Cell, 80, 631-638.

Lemer et al., 1996

Lemer, C., Rooman, M. J. &Wodak, S. J. (1996). Protein structure prediction by threading methods: evaluation of current techniques. Proteins, 23, 337-355.

Lipman &Pearson, 1985

Lipman, D. J. &Pearson, W. R. (1985). Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.

Lowe et al., 1995

Lowe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W. &Huber, R. (1995). Crystal structure of the 20s proteasome from archaeon T. acidophilum at 3.4 Å resolution. Science, 268, 533-539.

Lupas et al., 1994

Lupas, A., Koster, A. J., Walz, J. &Baumeister, W. (1994). Predicted secondary structure of the 20s proteasome and model structure of the putative peptide channel. FEBS Letters, 354, 45-49.

Matthews et al., 1994

Matthews, S., Barlow, P., Boyd, J., Barton, G., Russell, R., Mills, H., Cunningham, M., Meyers, N., Burns, N., Clark, N., Kingsman, S., Kingsman, A. &Campbell, I. (1994). Structural similarity between the p17 matrix protein of HIV-1 and interferon-. Nature, 370, 666-668.

Murzin et al., 1995

Murzin, A., Brenner, S. E., Hubbard, T. &Chothia, C. (1995). scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.

Orengo, 1994

Orengo, C. (1994). Classification of protein folds. Current Opinion Structural Biol. 4, 429-440.

Orengo et al., 1993

Orengo, C. A., Flores, T. P., Taylor, W. R. &Thornton, J. M. (1993). Identification and classification of protein fold families. Prot. Eng. 6, 485-500.

Perkins et al., 1994

Perkins, S. J., F., S. K., Williams, S. C., Haris, P. I., Chapman, D. &Sim, R. B. (1994). The secondary structure of the von willebrand factor type a domain in factor b of human complement by fourier transform infrared spectroscopy. J. Mol. Biol. 238, 104-119.

Pickett et al., 1992

Pickett, S. D., Saqi, M. A. S. &Sternberg, M. J. E. (1992). Evaluation of the sequence template method for protein structure prediction. Discrimination of the -barrel fold. J. Mol. Biol. 228, 170-187.

Pongor et al., 1994

Pongor, S., Hatsagi, Z., Degtyarenko, K., Fabian, P., Skerl, V., Hegyi, H., Murvai, J. &V., B. (1994). The SBASE protein domain library, release 3.0 - a collection of annotated protein-sequence segments. Nuc. Ac. Res. 22, 3610-3615.

Richards &Kundrot, 1988

Richards, F. M. &Kundrot, C. E. (1988). Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins, 3, 71-84.

Rost, 1995

Rost, B. (1995). TOPITS: threading one-dimensional preditions into three-dimensional structures. Proc. 3rd. Int. Conf. Intel. Sys. Mol. Biol. , 314-321.

Rost &Sander, 1993

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

Rost &Sander, 1994

Rost, B. &Sander, C. (1994). Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.

Russell &Barton, 1992

Russell, R. B. &Barton, G. J. (1992). Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins, 14, 309-323.

Russell &Barton, 1994

Russell, R. B. &Barton, G. J. (1994). Structural features can be unconserved in proteins with similar folds: An analysis of side-chain to side-chain contacts, secondary structure and accessibilty. J. Mol. Biol. 244, 332-350.

Russell et al., 1995

Russell, R. B., Copley, R. R. &Barton, G. J. (1995). Protein fold recognition from secondary structure assignments. Proc. 28th Hawaii. Int. Conf. Sys. Sci. IEEE Press, 5, 302-311.

Russell &Sternberg, 1995

Russell, R. B. &Sternberg, M. J. E. (1995). How good are we? Current Biology, 5, 488-490.

Sheridan et al., 1985

Sheridan, R. P., Dixon, J. &Venkataraghavan, R. (1985). Generating plausible protein folds by secondary structure similarity. Int. J. Pep. Protein Res. 25, 132-143.

Siddiqui &Barton, 1995

Siddiqui, A. S. &Barton, G. J. (1995). Continuous and discontinuous domains - an algorithm for the automatic-generation of reliable protein domain definitions. Prot. Sci. 4, 872-884.

Sippl, 1990

Sippl, M. J. (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.

Smith &Waterman, 1981

Smith, T. F. &Waterman, M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.

Smith-Brown et al., 1993

Smith-Brown, M. J., Kominos, D. &Levy, R. M. (1993). Global folding of proteins using a limited number of distance constraints. Prot. Eng. 6, 605-614.

Sonnhammer &Kahn, 1994

Sonnhammer, E. L. L. &Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Prot. Sci. 3, 482-492.

Sowdhamini &Blundell, 1995

Sowdhamini, R. &Blundell, T. L. (1995). An automatic method involving cluster-analysis of secondary structures for the identification of domains in proteins. Prot. Sci. 4, 506-520.

Sun et al., 1995

Sun, S., Thomas, P. D. &Dill, K. A. (1995). A simple protein folding algorithm using a binary code and secondary structure constraints. Prot. Eng. 8, 769-778.

Taylor, 1991

Taylor, W. R. (1991). Towards protein tertiary fold prediction using distance and motif constraints. Prot. Eng. 4, 853-870.

Wodak &Rooman, 1993

Wodak, S. J. &Rooman, M. J. (1993). Generating and testing protein folds. Current Opinion Structural Biol. 3, 247-259.

Zhou et al., 1995

Zhou, M., Ravichandran, K. S., Olejniczak, E. T., Petros, A. M., Meadows, R. P., Sattler, M., Harlan, J. E., Wade, W. S., Burakoff, S. J. &Fesik, S. W. (1995). Structure and ligand recognition of the phosphotyrosine binding domain of shc. Nature, 378, 584-592.