How to calculate relavent solvent accessibility of all of the lysine residues in human proteome ? I have read a paper which described that they used the AlphaFold Protein Structure Database to calculate this but they didn't describe how to calculate in detail. Is there any R based code to calculate this value ? Or any other web based tools?
Well, since RSA stands for a measure of residue solvent exposure it can be calculated by the division between the solvent accessible surface area (ASA) and the maximum solvent accessible surface area (MaxASA). MaxASA can be defined experimentally and indeed there are many publications with different values. So, if you have the 3D structure, you just have to calculate the ASA and divide for MaxASA (you need to choose the values). Nowadays, there are many programs which try to predict RSA. Recently, I have calculated RSA with proteins coming from AlphaFold using a program called DSSP, which defines secondary structure and calculates ASA from a pdb file. Then I used this code available in GitHub which use reference values for MaxASA and calculates RSA. All the results are in csv so it is easy to filter any part of specific interest like lysine residues in your case.
Another link to help you understand more: link
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can someone explain this step by step please?