lack of theoretical models in the PDB? why?
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4.7 years ago
rayoub ▴ 110

I'm reviewing the PDB data, being largely ignorant of molecular biology, I have a question regarding experimental models vs theoretical models. Why are there so few theoretical models in the PDB as opposed to experimental models based on x-ray crystallography and NMR, which make up the vast majority of structural models in the PDB?

Only 2% of the models are considered theoretical. In the advanced search there is no category to search for these theoretical models (except possibly 'other' when it comes to experimental method).

I understand they are less accurate. Is there a threshold of accuracy? How about another resource beside the PDB that provides access to these theoretical models for mining purposes or else for research on a particular molecule?

PDB Protein Structure • 976 views
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4.7 years ago
andreas.prlic ▴ 290

Back in 2002 it was decided to separate theoretical models from experimental ones. The few theoretical models that you found are very old PDB entries. I am not sure what is the percentage, but I'd be surprised to see 2% theoretical models in PDB. I don't think that number is right.

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Do you know if there is a database for uploading purely theoretical structures to?

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I saw the number somewhere on the PDB 101 site. It made me scratch my head. With your comment, I understand it to be a historical artifact. Thanks.

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