Systematic representation of protein folding patterns.

A tabular representation of protein folding patterns is described, which comprises information about the order along the chain of helices and strands of sheet, identifies the elements of secondary structure that interact, and indicates their relative orientation. These tableaux are intelligible to both people and computers, and support the application of algorithms for identification of proteins with similar folding patterns. Their inclusion in a database of protein structures would support investigations of structural relationships at the topological level.

[1]  U. Kulkarni-Kale,et al.  Sequence alignment approach to pick up conformationally similar protein fragments. , 1992, Journal of molecular biology.

[2]  M. Zuker,et al.  The alignment of protein structures in three dimensions. , 1989, Bulletin of mathematical biology.

[3]  O. Ptitsyn,et al.  Principal folding pathway and topology of all‐β proteins , 1979 .

[4]  C. Chothia,et al.  Helix to helix packing in proteins. , 1981, Journal of molecular biology.

[5]  C. Sander,et al.  A database of protein structure families with common folding motifs , 1992, Protein science : a publication of the Protein Society.

[6]  M G Rossmann,et al.  Comparison of protein structures. , 1985, Methods in enzymology.

[7]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[8]  A. Lesk,et al.  Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures. , 1994, Journal of molecular biology.

[9]  N. Go,et al.  Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. , 1992, Journal of molecular biology.

[10]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[11]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[12]  M. Levitt,et al.  Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core , 1993, Current Biology.

[13]  Alexey G. Murzin,et al.  General architecture of the α-helical globule , 1988 .

[14]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[15]  P Willett,et al.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.

[16]  A. Mclachlan.  Gene duplications in the structural evolution of chymotrypsin. , 1979, Journal of molecular biology.

[17]  W R Taylor,et al.  A local alignment method for protein structure motifs. , 1993, Journal of molecular biology.

[18]  R J Williams,et al.  Three-dimensional structure of acylphosphatase. Refinement and structure analysis. , 1992, Journal of molecular biology.

[19]  D. Stuart,et al.  A method for the systematic comparison of the three‐dimensional structures of proteins and some results , 1984 .

[20]  T. Blundell,et al.  Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. , 1990, Journal of molecular biology.

[21]  Peter Willett,et al.  Three-dimensional chemical structure handling , 1991 .

[22]  A. Lesk,et al.  Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis. , 1994, Journal of molecular biology.

[23]  M. Sundaralingam,et al.  Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-A resolution. , 1988, The Journal of biological chemistry.

[24]  Mark S. Johnson.  Comparison of protein structures , 1991 .

[25]  T. P. Flores,et al.  Identification and classification of protein fold families. , 1993, Protein engineering.

[26]  M. E. Karpen,et al.  Comparing short protein substructures by a method based on backbone torsion angles , 1989, Proteins.

[27]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[28]  L. Sieker,et al.  Active site structures of deoxyhemerythrin and oxyhemerythrin. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A V Finkelstein,et al.  The classification and origins of protein folding patterns. , 1990, Annual review of biochemistry.

[30]  Arthur M. Lesk,et al.  Protein Architecture: A Practical Approach , 1991 .

[31]  W R Taylor,et al.  Fast structure alignment for protein databank searching , 1992, Proteins.

[32]  C. Sander,et al.  Detection of common three‐dimensional substructures in proteins , 1991, Proteins.

[33]  R. Abagyan,et al.  A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structures. , 1988, Journal of biomolecular structure & dynamics.

[34]  Arthur M. Lesk,et al.  Boolean programming formulation of some pattern-matching problems in molecular biology , 1993 .

[35]  C. Branden,et al.  Introduction to protein structure , 1991 .

[36]  P Willett,et al.  Use of techniques derived from graph theory to compare secondary structure motifs in proteins. , 1990, Journal of molecular biology.

[37]  W Furey,et al.  Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution. , 1983, Journal of molecular biology.

[38]  H Weinstein,et al.  Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity , 1985, Biopolymers.

[39]  C. Chothia,et al.  Structural patterns in globular proteins , 1976, Nature.

[40]  C. Orengo,et al.  A rapid method of protein structure alignment. , 1990, Journal of theoretical biology.