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To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure Prediction: an algorithm predicts from linear (primary) sequence what the secondary structure may be —often incorrectly. This can be homology based, covariance, deep learning etc. But most commonly just the vector norm of ...


3

Your request is rather specific, so there is no tool... It is a straightforwards request though. I'd impose the requirement that the structures be solved and no predicted secondary structure. You can do it two ways if using Python. PDB After downloading all PDB structures, in python with PyMOL (installable with conda, tricky without) you'd do something ...


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There is some confusion in the question. Solvent accessibility of a residue, i.e. the area accessible to the solvent (water), depends on the 3D structure of the protein. It's not a property of an amino-acid (chemical compound such as alanine, leucine, ...). There may be a correlation -- amino-acids with hydrophobic side chains are more likely to be buried,...


1

This looks like a python problem and not a “biopython”problem. Check your file structures. Try giving a full path for 16pk.pdb These might help. https://stackoverflow.com/questions/17658856/why-am-i-getting-a-filenotfounderror https://stackoverflow.com/questions/18757127/windowserror-error-2-the-system-cannot-find-the-file-specified-is-not-resol


1

Hey i solve this simply by use of SOV alghoritm. https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment cheers


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