Protein Tertiary Structure Prediction Structural Bioinformatics.

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Protein Tertiary Structure Prediction Structural Bioinformatics
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Transcript of Protein Tertiary Structure Prediction Structural Bioinformatics.

  • Slide 1
  • Protein Tertiary Structure Prediction Structural Bioinformatics
  • Slide 2
  • Primary: amino acid linear sequence. Secondary: -helices, -sheets and loops. Tertiary: the 3D shape of the fully folded polypeptide chain The Different levels of Protein Structure
  • Slide 3
  • Predicting 3D Structure Comparative modeling (homology) Based on structural homology Fold recognition (threading) Outstanding difficult problem Based on sequence homology
  • Slide 4
  • Comparative Modeling Similar sequences suggests similar structure
  • Slide 5
  • Sequence and Structure alignments of two Retinol Binding Protein
  • Slide 6
  • Structure Alignments The outputs of a structural alignment are a superposition of the atomic coordinates and a minimal Root Mean Square Distance (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Low values of RMSD mean similar structures There are many different algorithms for structural Alignment.
  • Slide 7
  • Comparative Modeling Builds a protein structure model based on its alignment to one or more related protein structures in the database Similar sequence suggests similar structure
  • Slide 8
  • Comparative Modeling Accuracy of the comparative model is related to the sequence identity on which it is based >50% sequence identity = high accuracy 30%-50% sequence identity= 90% modeled