Use of techniques derived from graph theory to compare secondary structure motifs in proteins.

Keywords

Substructure, Graphics, Computer science, Graph isomorphism, Subgraph isomorphism problem

References

• The Protein Data Bank: a computer-based archival file for macromolecular structures.恵子 宮北 — 1977
• Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference Fourier analysis.Rmm Rob Smits, M Maarten Prins — 1976
• Structure of the calcium regulatory muscle protein troponin-C at 2.8 Å resolutionCamila Carneiro Da S. Caiado — 1985
• Carboxypeptidase A: a protein and an enzyme.Florante A. Quiocho, William N. Lipscomb — 1971
• The structure of papain.Joost P.H. Drenth, J.N. Jansonius, Roelof Koekoek — 1971
• Two-Angstrom crystal structure of oxidized Chromatium high potential iron protein.Charles W. Carter, Joseph Kraut, Stephan T. Freer — 1976
• A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing.A. Arnone, Claus Bier, F. Albert Cotton — 1971
• The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure.George N. Reeke, J.W. Becker, Gerald M. Edelman — 1977
• The three-dimensional structure of ribonuclease-S. Interpretation of an electron density map at a nominal resolution of 2 A.Harold W. Wyckoff, Demetrius Tsernoglou, A. W. Hanson — 1970
• The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding proteins.Doletha M. E. Szebenyi, Keith Moffat — 1986
• Strjcture of human plasma prealbumin at 2-5 A resolution. A preliminary report on the polypeptide chain conformation, quaternary structure and thyroxine binding.C. C. F. Blake, Michael J. Geisow, Ian D.A. Swan — 1974
• Structure of a bacterial ferredoxin.Elinor T. Adman, Larry C. Sieker, Lyle H. Jensen — 1973
• Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution.Jens J. Birktoft, D. M. Blow — 1972
• Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.Dino Moras, KW Olsen, M.N. Sabesan — 1977
• Structure and possible catalytic residues of Taka-amylase A.Y. Matsuura, Masami Kusunoki, Wakako Harada — 1982
• A Comparison of Some Measures for the Determination of Inter‐Molecular Structural Similarity Measures of Inter‐Molecular Structural SimilarityPeter Willett, Vivienne Winterman — 1986
• Substructure Search by Set Reduction.John Figueras — 1972
• A graphics model building and refinement system for macromoleculesT. Alwyn Jones — 1978
• The 14th barrel rolls outCyrus Chothia — 1988
• Crystal structure of human carbonic anhydrase C.Anders Liljas, K. K. Kannan, Per-Christer Bergstén — 1972

Cited by

• Three‐dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph‐theoretical techniquesJayne Hayes — 1992
• Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low‐resolution models博彰 山勢 — 2002
• Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing MotifsJ. Donald Johnson, R.L. Jolley — 2005
• Discovering Spatial Relationships Between Approximately Equivalent Patterns in Contact MapsHui Yang, Keith Marsolo, Srinivasan Parthasarathy — 2004
• 3-D Lookup: Fast Protein Structure Database Searches at 90% ReliabilityLiisa Holm, Chris Sander — 1995
• Clustering in life sciences.Ying Zhao, George Karypis — 2003
• Alignment of Flexible Protein StructuresMaxim Shatsky, Z Y Fligelman, Ruth Nussinov — 2000
• A Novel Method for Feature Identification of ProteinsChandrasekhar Mamidipally, Santosh Noronha, Sumantra Dutta Roy — 2007
• Application of Support Vector Machines in BioinformaticsJung‐Ying Wang — 2002
• An Investigation Of Gene Networks Influenced By Low Dose Ionizing Radiation Using Statistical And Graph Theoretical AlgorithmsSudhir Naswa — 2012
• Mathematical Methods for Protein Structure Analysis and DesignConcettina Guerra, Sorin Istrail — 2003
• Méthodes de détection des similarités structurales : caractérisation des motifs conservés dans les familles de structures pour l'annotation des génomes. (Structural similarity detection methods: characterisation of conserved motifs in protein structure families for genome annotation)M. Carpentier — 2005
• Labels and RelationsMarie‐Paule Lefranc — 2013
• Network analysis and molecular dynamics simulations to investigate the link between structure and function in intrinsically disordered proteins and transcription factors.Matteo Lambrughi — 2015
• Bioinformatics and Genome AnalysisHans‐Werner Mewes, Henrik Seidel, B Weiss — 2002
• Algorithmes pour la comparaison de structures moleculaires tridimensionnellesVincent Escalier — 1997
• Search for a New Description of Protein Topology and Local StructureLukasz Jaroszewski, Adam Godzik — 2000
• Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic RepresentationsAmit Pal Singh, Douglas L. Brutlag — 1997
• A protein taxonomy based on secondary structureGeorge D. Rose, Teresa M. Przytycka, Rajeev Aurora — 1999
• Prediction of protein function using statistically significant sub-structure discoveryCraig Lucas — 2007

Related papers

• Subgraph Isomorphism Detection Using a Code Based RepresentationIván Olmos, Jesús A. González, Mauricio Osorio — 2005
• Brief Announcement: A Parallel Algorithm for Subgraph IsomorphismRohan Yadav, Umut A. Acar — 2019
• GRAPH-SUBGRAPH ISOMORPHISM PROBLEM SOLVING FOR DESIGNING SPECIAL COMPUTERSMatviy Ilyashenko, A.A. Goldobin — 2012
• Algorithm for α-β Subgraph Isomorphism Problem on Uncertain GraphJianzhong Li — 2011
• Fast Subgraph Matching Strategies Based on Pattern-Only HeuristicsAntonino Aparo, Vincenzo Bonnici, Giovanni Micale — 2019
• GRAPH-SUBGRAPH ISOMORPHISM PROBLEM SOLVING FOR ORGANIZATION RESOURCES DISTRIBUTIONMatviy Ilyashenko — 2014
• Improvement of Messmer’s Approach to Subgraph Isomorphism DetectionShotaro Nishimura, Kaoru Katayama, Manabu Ohta — 2005