PROTEP: A Program for Graph-Theoretic Similarity Searching of the 3-D Structures in the Protein Data Bank

[1]  P Willett,et al.  Three‐dimensional structural resemblance between the ribonuclease H and connection domains of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques , 1993, FEBS letters.

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

[3]  Yvonne C. Martin,et al.  A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists , 1993, J. Comput. Aided Mol. Des..

[4]  Chris M. W. Ho,et al.  FOUNDATION: A program to retrieve all possible structures containing a user-defined minimum number of matching query elements from three-dimensional databases , 1993, J. Comput. Aided Mol. Des..

[5]  Peter Willett,et al.  Similarity searching in databases of three-dimensional molecules and macromolecules , 1992, J. Chem. Inf. Comput. Sci..

[6]  Thomas R. Hagadone,et al.  Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases , 1992, J. Chem. Inf. Comput. Sci..

[7]  J. Thornton,et al.  Depicting topology and handedness in jellyroll structures , 1992, FEBS letters.

[8]  P Willett,et al.  Three‐dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph‐theoretical techniques , 1992, FEBS letters.

[9]  Joachim Selbig,et al.  Analysis of protein sheet topologies by graph theoretical methods , 1992, Proteins.

[10]  I. Haneef,et al.  Defining topologigical equivalences in macromolecules , 1991 .

[11]  Andrew Smellie,et al.  Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads , 1991, J. Chem. Inf. Comput. Sci..

[12]  J. Selbig,et al.  Knowledge-based prediction of protein structures. , 1990, Journal of theoretical biology.

[13]  Eleanor M. Mitchell,et al.  Structural resemblance between the families of bacterial signal-transduction proteins and of G proteins revealed by graph theoretical techniques. , 1990, Protein engineering.

[14]  P Argos,et al.  Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation. , 1990, Journal of molecular biology.

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

[16]  G J Kemp,et al.  An object-oriented database for protein structure analysis. , 1990, Protein engineering.

[17]  A. Holmgren,et al.  Crystal structure of chaperone protein PapD reveals an immunoglobulin fold , 1989, Nature.

[18]  S. Kim,et al.  Crystal structures of two intensely sweet proteins. , 1989, Trends in biochemical sciences.

[19]  J. Thornton,et al.  Protein motifs and data-base searching. , 1989, Trends in biochemical sciences.

[20]  Hans-Dieter Höltje,et al.  A molecular modeling study on binding of drugs to calmodulin , 1989, J. Comput. Aided Mol. Des..

[21]  Peter Willett,et al.  Searching techniques for databases of protein secondary structures , 1989, J. Inf. Sci..

[22]  Peter Willett,et al.  Rapid geometric searching in protein structures , 1989 .

[23]  M J Sternberg,et al.  A relational database of protein structures designed for flexible enquiries about conformation. , 1989, Protein engineering.

[24]  P. C. Weber,et al.  Structure and assembly of protocatechuate 3,4-dioxygenase , 1988, Nature.

[25]  Cyrus Chothia,et al.  The 14th barrel rolls out , 1988, Nature.

[26]  Peter Willett,et al.  Algorithms for the identification of three-dimensional maximal common substructures , 1987, J. Chem. Inf. Comput. Sci..

[27]  P. Willett,et al.  Pharmacophoric pattern matching in files of 3d chemical structures: comparison of geometric searching algorithms , 1987 .

[28]  Christopher J. Rawlings,et al.  Reasoning about protein topology using the logic programming language PROLOG , 1985 .

[29]  D. K. Friesen,et al.  A combinatorial algorithm for calculating ligand binding , 1984 .

[30]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[31]  F. R. Salemme,et al.  Structural and functional diversity in 4-α-helical proteins , 1980, Nature.

[32]  S J Oatley,et al.  Structure of prealbumin: secondary, tertiary and quaternary interactions determined by Fourier refinement at 1.8 A. , 1977, Journal of molecular biology.

[33]  C. Blake,et al.  Protein–DNA and protein–hormone interactions in prealbumin: a model of the thyroid hormone nuclear receptor? , 1977, Nature.

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

[35]  C. D. Barry,et al.  The predicted structure of the calcium-binding component of troponin. , 1975, Biochimica et biophysica acta.

[36]  C. Bron,et al.  Algorithm 457: finding all cliques of an undirected graph , 1973 .

[37]  H. van der Wel,et al.  Isolation and characterization of thaumatin I and II, the sweet-tasting proteins from Thaumatococcus daniellii Benth. , 1972, European journal of biochemistry.

[38]  I. Haneef,et al.  A robust and efficient automated docking algorithm for molecular recognition. , 1992, Protein engineering.

[39]  D. Bonchev.  Chemical Graph Theory: Introduction and Fundamentals , 1991 .

[40]  Peter Willett,et al.  Upperbound procedures for the identification of similar three-dimensional chemical structures , 1989, J. Comput. Aided Mol. Des..

[41]  M. James,et al.  Two trifluoperazine‐binding sites on calmodulin predicted from comparative molecular modeling with troponin‐C , 1988, Proteins.

[42]  T. A. Jones.  Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. , 1985, Methods in enzymology.

[43]  Harry G. Barrow,et al.  Subgraph Isomorphism, Matching Relational Structures and Maximal Cliques , 1976, Inf. Process. Lett..