[SocBiN] Fwd: ELIXIR 3D-BioInfo Implementation Study application for integration of protein annotations in PDBe-KB

[Arne Elofsson]

Yours

Arne

-----------------------------------------
  Arne Elofsson                  Science for Life Laboratory
  Tel:+46-(0)70 695 1045   Stockholm University
  http://bioinfo.se/               Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
Bluesky: @bioinfo.se
Twitter/X: @arneelof
  Mastodon: @arneelof at fediscience.org
  Zoom: https://stockholmuniversity.zoom.us/my/arneelof/
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>

---------- Forwarded message ---------
From: Orengo, Christine <c.orengo at ucl.ac.uk>
Date: Sun, 1 Jun 2025, 12:49
Subject: ELIXIR 3D-BioInfo Implementation Study application for integration
of protein annotations in PDBe-KB
To: 3d-bioinfo at elixir-europe.org <3d-bioinfo at elixir-europe.org>
Cc: Sameer Velankar <sameer at ebi.ac.uk>, Jennifer Fleming <jfleming at ebi.ac.uk>,
R. Gonzalo Parra <gonzalo.parra at bsc.es>, Vincent Zoete
<vincent.zoete at sib.swiss>, arne.elofsson at gmail.com <arne.elofsson at gmail.com>,
Bohdan Schneider <bohdan at ibt.cas.cz>


Dear 3D-BioInfo Community

Thanks to those of you who attended our conference in Barcelona this March.
It was a great meeting with nearly 120 participants and very exciting talks.

At the conference we held an ELIXIR panel session when we discussed a
possible application for funding for an ELIXIR Implementation Study by the
3D-BioInfo community.

The ELIXIR call for these studies is now live and 3D-BioInfo will be
applying.

As mentioned in the Barcelona session, our study will be based on a series
of workshops to increase the interaction of groups developing protein
annotations (e.g. prediction of protein structural characteristics like
functional sites, disorder, PTs, etc) with the PDBe knowledge base
(PDBeKB).

The workshops will train researchers in building NextFlow workflows and
APIs to export their predicted data to the PDBe-KB where their annotations
will be widely disseminated via a web portal that integrates multiple
annotations for protein structures. More details are given in the links
below.

If you are interested in participating in this study and attending one or
more of the workshops, which will be held at the EBI in Hinxton, UK, please
check the links below and add your name. The links include the planned
application for funding, to which you can add comments, together with
background information.

Expression of Interest (EOI) for Implementation Study Funding
*https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7
<https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7>*

Background
*https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing
<https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing>*

Ideas
*https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0
<https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0>*

Participants list:
*https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0
<https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0>*

*Please add your name and details to the participant list in the google
docs.*

*We need to submit the application to the hub by June 15th* so please add
your name by then to help increase the chance this study will be funded.

It will also be possible to join the study after that date by adding your
name.

Thanks very much
Christine

On behalf of 3D-BioInfo coordinating team
Sameer Velankar, Arne Elofsson, Vincent Zoete, Bohdan Schneider, Gonzalo
Parra
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