Protein Structure Prediction. Charles Yan. Different Levels of Protein Structures. The primary structure is the sequence of residues in the polypeptide chain. Secondary structure is a local regularly occurring structure in proteins . Alpha helices B eta sheets Loops (Coils, Turns).
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Proteins are not assembled into their native structuresby a biological process, but folding is a purely physicalprocess that depends only on the specific amino acidsequence of the protein.
In general, comparative modeling consists of
Improving sequence comparisontechniques have broadened the scope of comparative modeling.
While 30% sequence similarity was considered to bethe threshold for successful comparative modeling, predictionsfor targets with as low as 17% sequence similaritywere made during the CASP4 experiment and 6% during CASP5.
The importanceof comparative modeling will continue to grow as the numberof experimentally determined structures grows steadily and,therefore, the number of sequences that can be related to aknown structure is growing.
Accuracy of secondary structure predictions.
Ab initio methods have recently received increased attentionin the prediction of loops.
Progress for all variants of computational protein structureprediction methods is assessed in the biannual, communitywideCritical Assessment of Protein Structure Prediction(CASP) experiments. In the CASP experiments, research groups are invitedto apply their prediction methods to amino acid sequencesfor which the native structure is not known but to be determinedand to be published soon.