[3dem] pdb for near-atomic resolution EM maps
Irina Gutsche
gutsche at embl.fr
Mon Dec 1 23:43:08 PST 2014
Dear all,
I would like to deposit a near-atomic resolution map (4.3A) and the
corresponding atomic model to the respective databases. Given recent
discussions about overinterpretation of the data I am wondering what
would be the best way to proceed.
Indeed, some bulky side chains are clearly visible and could be placed
with confidence, in particular in certain regions of the map (according
to ResMap local resolution ranges from 3.5A to above 6A), but most of
them not. And even the criteria of "visibility" and "confidence" are
subjective. The protein complex is of big pharmaceutical interest and I
suppose that if the complete pdb with all the side chains is deposited,
it may be downloaded and used for example for drug design, as a kind of
"absolute truth", which might be dangerous. However, deposit only the
c-alpha is probably too restrictive. Another option would be to deposit
only the side chains we are "sure about", but again, it's subjective,
and anyway we can only be "sure" at the given resoluition. So what would
be the most honest and unbiased way to share these results with the
scientific community, in particular with biologists who are not
necessarily aware of the overinterpretation/overfitting/validation/etc
issues in our field but who use our results to design their experiments?
Thank you very much for your all ideas and suggestions,
Best regards,
Irina Gutsche
CNRS, Grenoble,
France
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