Skip to main content
Article thumbnail
Location of Repository

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm

By Ryosuke LA Watanabe, Enrique Morett and Edgar E Vallejo
Topics: Methodology Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2474619
Provided by: PubMed Central

Suggested articles

Citations

  1. (1997). A Genomic perspective on protein families. Science
  2. (2002). A poweful non-homology method for the prediction of operons in prokaryotes. Bioinformatics
  3. (1995). A study of cross-validation and bootstrap for accuracy estimation and model selection.
  4. (2002). A tree kernel to analyse phylogenetic profiles. Bioinformatics
  5. (2000). Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
  6. COG clusters of orthologous groups database
  7. (2005). Dingledine R: Text mining biomedical literature for discovering gene-togene relationships: A comparative Study of algorithms.
  8. (2002). E: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res
  9. (2004). E: The Database of Interacting Proteins:
  10. (2004). EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acid Res
  11. (2002). Enzyme function less conserved than anticipated.
  12. (2002). Extraction of groups from phylogenetic profiles using independent component analysis. Genome Informatics
  13. (2002). Gama-Castro S: The EcoCyc Database. Nucleic Acids Res
  14. (2003). How well is enzyme function conserved as a function of pairwise sequence identity. Bioinformatics
  15. (2003). Identification of functional links between genes using phylogenetic profiles. Bioinformatics
  16. (2006). Inferring fuctional coupling of genes from phylogenetic profiles using the bond energy algorithm with genetic algorithms.
  17. (2000). Integrative analysis of protein interaction data.
  18. (2001). Koonin E: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res
  19. (2005). Krap P: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res
  20. (2004). Marcotte E: Protein interaction networks from yeast to human. Curr Opin Struct Biol
  21. (2004). Merino E: GeConT: gene context analysis. Bioinformatics,
  22. (1998). Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and TI ribonucleases.
  23. (2006). Morett E: Inferring fuctional coupling of genes from phylogenetic profiles using the bond energy algorithm. Automatic Function Prediction
  24. (2004). Mushegian Arcady R: Detection of evolutionarily stable fragments of cellular pathways by herarchical clustering of phyletic patterns. Genome Biology
  25. Problem Decomposition and Data Reorganization by a Clustering Technique. Op Res
  26. (1997). Recent enhancements to the Blocks Databases servers. Nucleic Acid Res
  27. (2005). Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Research
  28. (1990). Rousseeuw P: Finding Groups in Data: An Introduction to Cluster Analysis
  29. (2000). S: A network of protein-protein interaction in yeast.
  30. (1992). Submodel selection and evaluation in regression: The X-random case. International Statistical Review
  31. (2005). Subramaniam S: Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins
  32. System Biology New York:
  33. (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nature Biotechnology
  34. (2005). Systems Biology: From isolation to integration, a systems biology approach for building the Silicon Cell USA:
  35. (1997). TESS: a geometric hasing algorithm for deriving ED coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci
  36. (1990). The bond energy algorithm revisted.
  37. (2004). the enzyme database: updates and major new developments. Nucleic Acids Res
  38. The R Project for Statistica Toolkit [http://www.r-project.org/]
  39. (1984). Vertical partitioning of algorithms for database design.
  40. (2006). Vitkup D: Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol
  41. (1999). Yeates T: Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. PNAS
  42. (2000). Yeates T: Protein function in the post-genomic era. Nature

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.