[3dem] Announcing 3DBionotes-Covid-19

[Jose Maria Carazo]

Dear Colleagues,



As scientists, we are all trying to help, from our particular expertise, on
ways to better understand SARS-Covid-2 and the pandemic we are going
through. In our case, we work on image analysis and data management. Many
of you know us well from our software (XMIPP and Scipion), but all users of
EMDB at EBI, whenever they look at an entry, they also see the remark
"3DBionote available for this entry", and if you click on it you get into
an interactive environment where you can do your own "data mining" on
structures and annotations.



>From this background, we are happy to announce our new additional site
"3DBionotes-Covid-19", fully focused on the pandemic, that you can find at:



https://urldefense.com/v3/__http://3dbionotes.cnb.csic.es__;!!Mih3wA!TQ7phFRnvSnoBOdxC3WmqF7Va6TB53A8nnGr5djbkA0Yq8r5vV8K2rYL86kZZ0oA_A$ 



and then selecting the green option Covid-19



It starts "small" and far from perfect, but it will grow as we get more
data and we interoperate with other resources. As always, this development
is only possible because "we stand on the shoulders of giants", and we
acknowledge the great work of Andrea Thorn's team at
https://urldefense.com/v3/__https://github.com/thorn-lab/coronavirus_structural_task_force__;!!Mih3wA!TQ7phFRnvSnoBOdxC3WmqF7Va6TB53A8nnGr5djbkA0Yq8r5vV8K2rYL86kTKu3SbA$ , from where
we take their refined structural models, so that within 3DBinotes-Covid19
you can always choose to work on the regular PDB model or, instead, on
PDB-redo or Isolde-analyzed models. And, of course, our colleagues at EMDB,
PDBe, Uniprot .... (and, in general, the work at EBI/ELIXIR) since without
them 3DBionotes would not be possible. Expect a closer integration with
PDB-KB Covid-19 efforts very soon (PDB in Europe Knowledge Base)



In this first release we have worked hard to offer you some genomics
variants analysis, knowing that it is just a start and that, surely, there
will be many more sources of information in the near future that will be
subsequently incorporated. We also want to stress the crucial task of
compound screening, and we start in this first release with the three
Fragment Based Screening experiments performed at Diamond in the context of
Instruct.UK; of course, we need to grow a lot in this area. As a last
remark, and since we are coming from cryo EM, we are including cryo EM
validation information, an area in which we actively develop methods and
that is particularly important considering the pace of results coming from
this field.


Please, check by yourself this very first implementation, which will be
substantially expanded in the coming weeks. We would love to know from you
about new initiatives we could interact with, since it is really time to
work together



With best wishes.... The 3DBionotes-Covid19 team

-- 
Prof. Jose-Maria Carazo
Biocomputing Unit, Head
Instruct cryoEM Image Processing Center (I2PC), Director
INB/ELIXIR.ES CNB Node, Director
Spanish National Center for Biotechnology, CNB-CSIC
Darwin 3, Campus Universidad Autonoma de Madrid
28049 Madrid, Spain


Cell: +34639197980
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