Methods for Protein Structure Prediction - Fox Chase Cancer Center

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Comparative Modeling Basic Protocol 1. Identification of homologue for target sequence 2. Alignment of target sequence to template sequence and structure 3. Side-chain modeling, copy the backbone of the template and model the new side chains onto this backbone 4. Loop modeling, for insertions and deletions in the alignment 5. Refinement of model -- moving template closer to target 6. Assessment of (predicted) model quality 7. Using the model to explain experiments and guide new ones
Identification and Alignment Search the Protein Data Bank (http://www.rcsb.org) for proteins of known structure homologous to target Using: BLAST (identity>40%) PSI-BLAST (identity>15-20%) Profile-profile alignment methods (identity>5-10%) Fold recognition methods (identity>5-10%) Meta-methods that combine many FR and PP servers Manual improvements in alignment according to structure of template
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Page 11: Hints at function Human SULT4A1 Sul
Page 15 and 16: Loop modeling Shift in loop Deletio
Page 17 and 18: Always requires: Prediction at Each
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Page 21 and 22: 2900 licenses in 73 countries SCWRL
Page 23 and 24: Future technologies • Modeling of
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