Protein Fold References
Brenner, S. E., Chothia, C., Hubbard, T. J. and Murzin, A. G. (1996). Understanding protein structure: using scop for fold interpretation. Methods Enzymol, 266, 635-43.
Bryant, S. H. and Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins, 16(1), 92-112.
Chothia, C. (1992). One thousand folds for the molecular biologist. Nature 257:543-544.
Chothia, C. and Lesk, A. M. (1986). The relation between the divergence of sequence and structure in proteins. Embo J, 5(4), 823-6.
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Chothia, C., Lesk, A. M., Levitt, M., Amit, A. G., Mariuzza, R. A., Phillips, S. E. and Poljak, R. J. (1986). The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science, 233(4765), 755-8.
Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith, G. S., Air, G., Sheriff, S., Padlan, E. A., Davies, D., Tulip, W. R. and et, a. l. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342(6252), 877-83.
Crippen, G. M. (1996). Failures of inverse folding and threading with gapped alignment. Proteins, 26(2), 167-71.
Fischer, D., Rice, D., Bowie, J. U. and Eisenberg, D. (1996). Assigning amino acid sequences to 3-dimensional protein folds. Faseb J, 10(1), 126-36.
Holm, L. & Sander, C. (1996). The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Research 24(1):206-209.
Johnson, M. S., May, A. C., Rodionov, M. A. and Overington, J. P. (1996). Discrimination of common protein folds: application of protein structure to sequence/structure comparisons. Methods Enzymol, 266, 575-98.
Jones, D. and Thornton, J. (1993). Protein fold recognition. J Comput Aided Mol Des, 7(4), 439-56.
Jones, D. T., Miller, R. T. and Thornton, J. M. (1995). Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins, 23(3), 387-97.
Lesk, A. (1991). Protein Architecture: A Practical Approach . Oxford: IRL Press at Oxford University Press.
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Lesk, A. M. and Chothia, C. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol, 136(3), 225-70.
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Miller, R. T., Jones, D. T. and Thornton, J. M. (1996). Protein fold recognition by sequence threading: tools and assessment techniques. Faseb J, 10(1), 171-8.
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Rice, D. W. and Eisenberg, D. (1997). A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol, 267(4), 1026-38.
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Protein Structure Superposition References
Arun, K.S., Huang, T.S., & Blostein, S.D. (1987). Least-squares fitting of two 3-D point sets. IEEE Transactions on Pattern Analysis and Machine Intelligence 9(5), 698-700.
Barakat, M.T. & Dean, P.M. (1991). Molecular structure matching by simulated annealing, III. The incorporation of null correspondences into the matching problem. J. Comp.-Aided Mol. Design, 5, 107-117.
Bashford, D., Chothia, C, & Lesk, A.M. (1987). Determinants of a protein fold: Unique features of the globin amino acid sequences. J. Mol. Biol., 196, 199-216.
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Orengo, C.A. & Taylor, W.R., 1996. SSAP: Sequential Structure Alignment Program for protein structure comparison. Meth. in Enzym., 266, 617-635.
Orengo C.A., Flores, T.P., Taylor, W.R., & Thornton J.M. (1993). Identification and classification of protein fold families. Protein Eng., 6, 485-500.
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Sali, A. & Blundel, T. (1990). Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403-428.
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Taylor, W. & Orengo, C. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
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Zuker, M. and Somorjai, R.L. (1989). The alignment of protein structures in three dimensions. Bull. Math. Biol., 51(1), 55-78.
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