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I've got some predcited protein structures, and I want to see how well they match against another one from the Protein Databank. See the attached files. I-TASSER and EsyPred3D and predict protein were all used. What I designed was an ScFv, and now I need to see how similair it is to something else. I have no idea what I;m doing other than that. The text document is the peptide sequence I designed. Any help appreciated.. I-TASSER results for your_protein.zip ESyPred3D.zip sequence (bad areas removed).txt

Not very big, here it is: >QVQLQQSGGGLVQPGGSLKLSCAASGYTFSSYWMGWVRQAPGKGLEWVGWINPGGGGTSYAQSVKGRFTISADKSSNTAYLQMNSLKPEDTAVYYCARRASYRSNNYRYWGQGTQVTVSSGGGGSGGGGSGGGGSDIELTQSPPSVSVSPGQRVTITCRASSSIGNSYLHWYQQKPGQAPKLLIYGTSNLVSGVPDRFSGSGSGTSFSLTISSLEAEDVAVYYCQQYNSSPPTFGGGTKLEVKR

I've designed an scFv against Indole acetic acid. I haven't got access to any lab equipment (this is a desk based project), so I've been told I have to use some kind of prediction software to see how well this scFv will bind. I've only designed the primary peptide sequence. How would I go about doing this? I would imagine I'd need some kind of programme that can show me how this peptide sequence I've made fits to Indole acetic acid. But I don't think it's possible to predict tertiary protein structure just from the peptide sequence. I've heard about PYMOL and some bioserf thing on UCL, but I really haven't got any experience using these things, and don't know what the results mean! I did something with that predictprotein.org site but don't know what the results mean.