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Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring ...


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At this point, it must be verified experimentally. In this foldit research paper, they use software and user input to design essentially an enhanced version of a naturally occurring protein, but they then physically make their new protein and determine its structure experimentally, using x-ray crystallography. Overall, they use a lot of trial and error ...


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3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


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That depends on what your are trying to do. Apparently your query sequence is similar to that of proteins with a known 3D-structure. As it says on Jpred's result page (and help), in this case it might be worth looking at these homologues with experimentally determined structures for information on secondary structure. Most likely it will be more accurate ...


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Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary ...



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