Interpreting the Protein Structure Prediction overview image.

Example Image:

About the image:
This overview image is meant to supply a snapshot of predicted structural information about the protein sequence. A legend on the right-hand side of the image indicates what data that section of the image is displaying. The image consists of the following sections:

• SS - Secondary Structure: Secondary structure is predicted using PsiPred--a secondary structure prediction method that uses feed-forward neural networks and PSI-BLAST. α-helices are shown in red, and β-sheets are shown in blue.
  • Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
• D - Disordered Regions: DISOPRED is used to identify disordered regions.
  • Jones, D.T. & Ward, J.J. (2003) Prediction of Disordered Regions in Proteins from Position Specific Score Matrices. Proteins, 53 Suppl 6, 573-578.
• TM - Transmembrane Regions: TMHMM is used to identify transmembrane regions.
  • A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. "Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes." JMB, 305(3):567-580, January 2001.
  • E. L.L. Sonnhammer, G. von Heijne, and A. Krogh. A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.]
• CC - Coiled Coil Regions: COILS is used to identify coiled-coil regions.
  • Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coiled Coils from Protein Sequences, Science 252:1162-1164.
• SP - Signal Peptide: Signal peptides are predicted using SignalP, which predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.
  • Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne and Søren Brunak. J. Mol. Biol., 340:783-795, 2004.
• Domain Parse Schematic: Next follows a cartoon that graphically displays the predicted domains using a linear representation of the protein. Domains are distinguished from neighboring domains using separate colors. These domains are described in more detail in the table underneath the graphic on the protein overview page.

• PS - Position Specific Scoring Matrix: A value determined by PSI-BLAST for each position, indicating the level of conservation of residues at that position.
• Multiple Sequence Alignment: A graphical representation where protein sequences determined by PSI-BLAST are aligned..

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