 Dear students, now we will see how threading or fold recognition works in the form of a flow chart, but before we do that Let's take an overview of what fold recognition threading was. It's simply involved Passing the sequence that is the amino acid sequence over a structure So this structure is a fold from the fold library such as SCARP and Now if you're passing the sequence onto the fold Then you find that fold which best matches the sequence that you have with you Next is you give it a score using some scoring function, which is typically a z-score function Now let's take a look at the overall flow chart for threading in a step-by-step manner So the inputs and outputs first So the inputs were the folds from fold library such as SCARP, the amino acid sequence, the primary sequence of the protein You want to create the structure for or predict the structure for the scoring function This is input into your threading algorithm and the output is your predicted structure. Okay Now let's start. So you have your amino acid sequence of Proteins of course. So this is the protein whose structure is unknown so structure is Unknown Sequence is known Okay, so next You blast this sequence to obtain homologs. So you have your sequence and And You blast it So this is your target sequence and these are your templates so you compare it by using blast with all of these sequences and You find those sequences which are Nicely matching to your target Next you extract the template structures from the PDB So for example if you had these sequences That matched very nicely and therefore became the templates template sequences So now you have to extract their structures So these sequences may have different structures which you can look at from the PDB So you simply go and find the structure for each one of these sequences in the PDB after this you go to the Fold database such as scop to obtain the folds for each template So let's say if you had this structure for a protein and You obtained its PDB in this step then you go to the scop database and You obtain the various Folds That combine to give you This complete structure so each one of them is a fold and now you can Individually deal with these folds What we will do with these folds is as follows so we compare The predicted structures that is fold with the experimental homologs now if the structure is Functional and plausible both of them then you create a tertiary structure by combining these folds So you can select one fold from one PDB Another fold from some other PDB some other structure some other fold from yet another PDB and combine them to create and predict the structure for the sequence. You're looking for here is the summary of this So these are two very different proteins But the common thing between them is this structure That is given here which contains several folds As shown here and now you're trying to compare your sequence With a specific portion in the fold So by comparing them You can find out which fold best matches which portion of the sequence So therefore your overall structure will be a combination of folds from different structures in the PDB So now to conclude Your secondary structure combinations They come together to create these folds And different folds they come together yet again to create the overall tertiary structure of the protein So in fold recognition or threading your job is simply to find out which fold in a specific protein matches your sequence and by taking these different folds from different protein structures You create a collection of folds and you bring them together to create a tertiary structure for the protein