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It allows us to find where secondary structural elements ( α helices, β sheets, loops) are located. Secondary Structure Predictors Chou-Fasman COMBINE GORIII PRISM PHD0 PHD3 PSIPred PSIPred uses most recent algorithm that can predict secondary structure of about 80% accuracy. Protein Threading or Protein Fold Recognition Although proteins are of large no, tertiary structural motifs are limited to which most protein belongs. It is speculated that about 1000 distinct protein folding patterns may be present in total. Surprisingly, a few dozen folding patterns account for about half of all known protein structures . This helps to use previously solved structures as starting point. To identify the fold the sequence is compared with all 500+ folds in library of known protein structure . If pair-wise alignment shows less than or nearly 30% identity then it is ideal to be used for protein fold recognitions. When successful, structure from fold recognition may be about 3-6Å RMSD (root mean...

Why prediction of protein structure important ? You may ask what is there in protein structure?? That is because structure determines function of the protein. Take the example of enzyme dehydrogenases. It has an NAD-binding site called Rossaman fold ( Dinucleotide binding fold). This fold is made up a pair of βαβαβ subunit. Thus if a protein contain a βαβαβ subunit than it acts as a binding site for a nucleotide . Structure is better conserved than sequences in protein during the course of evolution e.g. take the example of Cytochrome C of eukaryotes and C-cytochromes of prokaryotes in different species(which change with evolution in prokaryotes) where all perform general functions i.e. electron carrier. But different species exibit low degree of similarity of sequence to each other and to that of eukaryotes. They also differ in polypeptide loops on surface . But X-Ray structure are similar particularly chain folds and side chain packing to interior . We require structural knowl...