Practical (I) Prediction of binding sites and other functional regions of the Ras oncogene based on multiple sequence alignments

• Data
  • Sequence: 5p21.seq
  • Multiple sequence alignment: [HSSP] [MSF] [MUL]
  • 3D structure: [PDB]
  • Secondary structure and accessibility definition: [DSSP]

• Servers & programs
  • ClustalW www interface @CNB (Multiple sequence alignment).
  • Blast www interface @NCBI (Sequence searches).
  • TreeDet server @CNB: http://pdg.cnb.uam.es/servers/treedet/
  • Protein interaction site prediction @Bologna: http://gpcr.biocomp.unibo.it/cgi/predictors/pp/pred_pp.cgi

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• Some results
  • MTreedet (treedet + conservation -entropy-). Correlation plot for position 37.
  • Treedet server (Mtreedet S-method & others) (local version).
  • Protein interaction site prediction results.
  • Conservation (HSSP VAR).

• Additional Data
  • Ras complexes of known structure: 1gua.pdb / 1bkd.pdb / 1wq1.pdb.

• Additional Servers & Programs
  • Evolutionary Trace server @Cambridge. ET method (see theoretical part).
  • ConSurf server @Israel. Evolutionary weighted conservation maped on 3D structures.
  • ConSeq server @Israel. Evolutionary weighted conservation combined with PREDICTED solvent accessibility.
  • SDPred server @Rusia. Prediction of amino acid residues that determine differences in functional specificity of homologous proteins. (supervised method).

  • RasMol for various platforms - RasWin (local copy)