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Geometric Hashing Of Pdb Structures?

Joerg asked on the Blue Obelisk eXchange about geometrical hashing of PDB files. As there have not been any answers from the open source cheminformatics community yet, I am copying his question here:

    Can anyone point me to geometric hashing options for PDB files? I am mainly interested in comparing two PDB files as fast as possible, and I need a comparison being more elaborate than just a Calpha comparison.
pdb structure similarity
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updated by Chris • Chris • written by Egon Willighagen Egon Willighagen

2 answers

For comparing PDB structures the first options (in order of sensitivity) that come to mind are:

These are often used to calculate the similarity between a predicted structure and native native in experiments like CASP.

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written by Kraut Kraut

@Adam: Do you know about any tool/server that can calculate GDT scores ?

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written by Khader Shameer Khader Shameer

Perhaps protein structure alignment is what you're looking for. Famous algorithms are e.g. DALI and CE.

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written by Chris • Chris

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