Articles listed here are mainly concerned with principles
that govern secondary structure associations and chain topology,
and the use of these principles to classify protein structures.
Papers on methods for detecting structural similarities are
reviewed in Orengo (1994) and
Holm & Sander (1994).
Sternberg, M.J.E. & Thornton, J.M. (1976) On the conformation of proteins: the handedness of the beta-strand - alpha-helix - beta-strand unit J. Mol. Biol. 105, 367-382.
Richardson, J.S. (1976) Handedness of crossover connections in beta-sheets Proc. Natl. Acad. Sci. USA 73, 2619-2623.
Chothia, C., Levitt, M. & Richardson, D. (1977). Structure of proteins: packing of alpha-helices and beta-sheets. Proc. Natl. Acad. Sci. USA 74, 4130-4134.
Richardson, J.S. (1977). Beta-sheet topology and the relatedness of proteins. Nature 268, 495-500.
Janin, J. (1979). The protein kingdom: a survay of the three dimensional sutucture and evolution of globular proteins. Bull. Inst. Pasteur 337-373.
Ptitsyn, O.B. & Finkelstein, A.V. (1981). Similarities in protein topologies: evolutionary divergence, functional convergence or principles of folding. Q. Rev. Biophysics. 13, 339-386.
Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Prot. Chem. 34, 167-339.
Chothia, C. (1984). Principles that determine the structure of proteins. Ann. Rev. Biochem. 53, 537-572.
Finkelstein, A.V. & Ptitsyn, O.B. (1987). Why do globular proteins fit the limited set of folding patterns. Prog. Biophys. Mol. Biol. 50, 171-190.
Orengo, C. (1994). Classification of protein folds. Curr. Opin. Struct. Biol. 4, 429-440.
Russell, R.B. & Barton, G.J. (1994). Structural features can be unconserved in proteins with similar folds. J. Mol. Biol. 244, 332-350.
Blundell, T.L. & Johnson, M.S. (1993). Catching a common cold. Protein Sci. 2, 887-883.
Chothia, C. & Finkelstein, A.V. (1990). The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59, 1007-1039.
Grindley, H.M, Artymiuk, P.J., Rice, D.W. & Willett, P. (1993). Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
Holm, L, Ouzounis, C., Sander, C., Tuparev, G., Vriend, G. (1993). A database of protein structure families with common folding motifs. Protein Sci. 1, 1691-1698.
Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
Holm, L. & Sander, C. (1994). Searching protein structure databases has come of age. Proteins 19, 165-173.
Murzin, A. G. (1994). New protein Folds. Curr. Opin. Struct. Biol. 4, 441-449.
Overington, J.P., Zhu, Z.Y., Sali, A., Johnson, M.S., Sowdhamini, R., Louie, C. & Blundell, T.L. (1993). Molecular recognition in protein families: a database of three-dimensional structures of related proteins. Biochem. Soc. Trans. 21 597-604.
Orengo, C., Flores, T.P., Taylor, W.R., Thornton, J.M. (1993). Identifying and classifying protein fold families. Protein Eng. 6, 485-500.
Pascarella, S. & Argos, P. (1992). A data bank merging related protein structures and sequences. Protein Eng. 5, 121-137.
Sali, A. & Blundell, T.L. (1990). The 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.
Taylor, W.R. & Orengo, C.A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
Yee, D.P. & Dill, K.A. (1993) Families and the structural relatedness among globular proteins. Protein Sci. 2, 884-899.
Connolly, M.L., Kuntz, I.D. & Crippen, G.M. (1980). Linked and threaded loops in proteins. Biopolymers 19, 1167-1182.
Efimov, A.V. (1982). Supersecondary structure of beta-proteins. Mol. Biol. 16, 799-806.
Efimov, A.V. (1994) Favoured structural motifs in globular proteins. Structure 2 999-1002.
Finkelstein, A.V. & Ptitsyn, O.B. (1979). Folding and topology of the antiparallel beta-structure. Biofizika 24, 21-26.
Hutchinson, E.G. & Thornton, J.M. (1993). The Greek Key motif: extraction, classification and analysis. Protein Eng. 6, 233-245.
Klapper, M.H. & Klapper, I.Z. (1980). The "knotting" problem in proteins: loop penetration. Biochim. Biophys. Acta 626, 97-105.
Presnell, S.R. & Cohen, F.E. (1989). Topological distribution of four alpha-helix bundles. Proc. Natl. Acad. Sci. 86 6592-6596.
Ptitsyn, O.B. & Finkelstein, A.V. (1979). Folding and topology of the parallel beta-structure. Biofizika 24, 27-31.
Sternberg, M.J.E. & Thornton, J.M. (1977) On the conformation of proteins: the handedness of the connection between parallel beta-strands. J. Mol. Biol. 110, 269-283.
Sternberg, M.J.E. & Thornton, J.M. (1977) On the conformation of proteins: an analysis of beta-pleated sheets. J. Mol. Biol. 110, 285-296.
Woolfson, D.N., Evans, P.A., Hutchinison, E.G. & Thornton, J. (1993) Topological and stereochemical restrictions in beta-sandwich protein structures. Prot. Eng. 6, 461-470.
Crick, F.H.C. (1953). The packing of alpha-helices: simple coiled coils Acta Crystallogr. 6 , 689-697.
Harris, N.L., Presnell, S.R. & Cohen, F.E. (1994). Four helix bundle diversity in globular proteins. J. Mol. Biol. 236, 1356-1368.
Murzin, A.G. & Finkelstein, A.V. (1988). General architecture of the alpha-helical globular J. Mol. Biol. 204, 749-770.
Weber, P.C. & Salemme, F.R. (1980). Structural and functional diversity in 4-alpha-helical proteins. Nature 287, 82-84.
Janin, J. & Chothia, C.(1981). Packing of alpha-helices onto beta-pleated sheets and the anatomy of alpha/beta proteins. J. Mol. Biol. 143, 95-128.
Orengo, C.A. & Thornton, J.M. (1993). Alpha plus beta folds revisited: some favoured motifs. Structure 1 105-120.
Cohen, F.E., Sternberg, M.J.E. & Taylor, W.R. (1981). Analysis of the tertiary structure of protein beta-sheet sandwiches. J. Mol. Biol. 148, 253-272.
Lasters, I., Wodak, S.J. Alard, P. & Van Cutsem, E. (1988). Structural principles of parallel beta-barrels in proteins. Proc. Natl. Acad. Sci. USA 85, 3338-3342.
Lasters, I., Wodak, S.J. & Pio, F. (1990). The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements. Proteins, 7, 249-256.
Lesk, A.M., Brändén, C.-I. & Chothia, C. (1989). Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet. Proteins, 5, 139-148.
McLachlan, A.D. (1979). Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol. 128, 49-79.
Murzin, A.G., Lesk, A.M. & Chothia, C. (1992). beta-trefoil fold. J. Mol. Biol. 223, 531-543.
Murzin, A.G., Lesk, A.M. & Chothia, C. (1994). Principles determining the structure of beta-sheet barrels in proteins: I a theoretical analysis. J. Mol. Biol. 236, 1369-1381.
Murzin, A.G., Lesk, A.M. & Chothia, C. (1994) Principles determining the structure of beta-sheet barrels in proteins: II the observed structures. J. Mol. Biol. 236 1382-1400.
Novotny, J., Bruccoleri, R. E. & Newell J. (1984). Twisted hyperboloid (Strophoid) as a model of beta-barrels in proteins. J. Mol. Biol. 177. 567-573.
Salemme, F.R. & Weatherford, D.W. (1981). Conformational and geometrical properties of beta-sheets in proteins: I parallel beta-sheets. J. Mol. Biol. 146 101-117.
Salemme, F.R. & Weatherford, D.W. (1981). Conformational and geometrical properties of beta-sheets in proteins: II antiparallel and mixed beta-sheets. J. Mol. Biol. 146, 119-141.
Salemme, F.R. (1981). Conformational and geometrical properties of beta-sheets in proteins: III isotropically stressed configurations. J. Mol. Biol. 146 143-156.