Protein Tertiary Structure Prediction
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
This unit addresses how to predict the tertiary structure of a protein from its amino acid sequence using computational methods. Three types of prediction methods??homology modeling, fold recognition, and ab initio prediction??are introduced.
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- Homology Modeling
- Sequence Profile Methods
- PSI‐BLAST
- Threading
- Ab Initio Prediction
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 2.7.1 A comparison between the predicted structure using MODELLER (thick lines) and the experimental structure (thin lines) for CASP‐3 targets t0074 (A ) and t0068 (B ). This figure was made using visual molecular dynamics (VMD; Humphrey et al., ). View Image -
Figure 2.7.2 The first iteration result of PSI‐BLAST for the CASP‐3 target t0081. The entries above the “Run PSI‐Blast iteration 2” button will be used by the default (with the EXPECT value, listed at the end of each entry, <0.001). The entries below the button are optional to use in the search of the next iteration. View Image -
Figure 2.7.3 A comparison between predicted (A ) and experimental (B ) structures for the CASP‐3 target t0053. Cylinders indicate α helices, strands indicate β sheets, dark lines indicate turns, and thin lines indicate loops. This figure was made using the INSIGHT II package (Molecular Simulations, ). View Image -
Figure 2.7.4 A comparison between predicted (A ) and experimental (B ) structures for the CASP‐3 target t0067. Cylinders indicate α helices, strands indicate β sheets, dark lines indicate turns, and thin lines indicate loops. This figure was made using the INSIGHT II package (Molecular Simulations, ). View Image
Videos
Literature Cited
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