Modification Rmsd Script In Terms Of Database Concepts

Question

[Priyanka]

Dear Friends,

I am comparing one (query) pdb file with all the pdb files in the folders and returning the RMSD value and for which I have written a script. Now I want the (folder) pdb files to be stored as a database and when the user provides the query pdb file, it should compare with all the pdb files present in the database. How can I modulate my script in terms of database?

I am very new to this database concept. So, this might be a silly question for few of the pioneers in biostar.

Thanks in advance

Answer 1

[Istvan Albert]

A database is a very a broad concept, a directory is already a database as it optimizes access to a file. Just storing a pdb in a database does not get you any benefit. If all you wanted is to access a file then it will be slower to fetch from the database than iterate over a directory.

What I suspect that you might be after is some sort of database query mechanism that finds the most similar structure but without having to recompute the RMSD for every structure. That is a very difficult problem and solving it probably requires substantial effort. I don't work in this field but I am pretty sure that there are several published papers that deal with fast 3D structure comparisons and I would advise to search the literature for existing methods.