Dear Pavel and Oliverio,
In our group we have had recent discussion about this issue, and I
second Pavel's suggestion to introduce such a confidence measure.
When interpreting cryo-EM (but also X-ray crystallography) maps with
models, we often face the problem that we have complete models (thanks
to Alphafold) but incomplete density. Most often the lack of density is
due to conformational flexibility. So the question is what to do with
those parts that lack map support? Some favor the option not to model
these parts. However, usually we are pretty certain that these parts are
present, but too flexible to be observed. So I personally think that
structural models should be deposited as complete as possible.
Having such a confidence measure would facilitate the interpretation of
our structural models, also because it seems that not many actually open
the associated deposited maps/densities when interpreting deposited
structures.
Best wishes,
Tim
On 2025-03-04 00:27, Pavel Afonine wrote:
Greetings,
It's hard to disagree with this! Resolution, occupancies, and B
factors only indirectly suggest what's visible and what isn't — and
they can be especially difficult to interpret correctly for
non-specialists. Perhaps a local confidence measure — similar to pLDDT
for predicted models — could address this by condensing into a single
number everything we know about the model quality and how well it fits
the data, computed per atom or per residue.
All the best,
Pavel
On Mon, Mar 3, 2025 at 7:21 AM Italo Carugo Oliviero
<olivieroitalo.car...@unipv.it> wrote:
A brief reflection on IDPs
Increasingly, people with a computer science background are
analyzing the data deposited in the Protein Data Bank. In the case
of conformation disorder analyses, they consider residues that are
explicitly stated to be disordered (the old REMAR 465 records).
This is not quite correct as there are two problems.
- The first is that some crystallographers consider “visible,” and
deposit their coordinates, even amino acids that have
stratospheric B-factors, so large as to indicate that those amino
acids are definitely “invisible” in electronic density maps.
- The second problem has to do with crystallographic resolution.
The amount of “invisible” amino acids increases as the
crystallographic resolution decreases. At low resolution, electron
density maps are often not very detailed, and some parts of them
cannot be interpreted. But this does not mean that the amino acids
found there are definitely “invisible.” It simply means that
resolution might be insufficient.
Editors and reviewers may find it useful to keep these
considerations in mind when evaluating articles on conformational
disorder submitted by scientists that lack a structural
biologybackground. Or is there something else that can be done?
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