<div dir="auto"><div><br></div><div><br></div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"> <br>Yours<br><br>Arne<br><i><br></i>-----------------------------------------<br> Arne Elofsson Science for Life Laboratory<br> Tel:+46-(0)70 695 1045 Stockholm University<br> <a href="http://bioinfo.se/" target="_blank">http://bioinfo.se/</a> Box 1031, <br> Email: <a href="mailto:arne@bioinfo.se" target="_blank">arne@bioinfo.se</a> 17121 Solna, Sweden<br></div><div>Bluesky: @<a href="http://bioinfo.se" target="_blank">bioinfo.se</a> </div><div dir="ltr">Twitter/X: @arneelof<br></div><div dir="ltr"> Mastodon: @<a href="mailto:arneelof@fediscience.org" target="_blank">arneelof@fediscience.org</a><br></div><div dir="ltr"> Zoom: <span style="display:inline-flex"><a href="https://stockholmuniversity.zoom.us/my/arneelof/" target="_blank">https://stockholmuniversity.zoom.us/my/arneelof/</a><span></span></span><br> Scholar: <a href="http://scholar.google.se/citations?user=s3OCM3AAAAAJ" target="_blank">http://scholar.google.se/citations?user=s3OCM3AAAAAJ</a><br> ORCID: <a href="https://orcid.org/0000-0002-7115-9751" target="_blank">0000-0002-7115-9751</a></div></div></div></div></div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">Orengo, Christine</strong> <span dir="auto"><<a href="mailto:c.orengo@ucl.ac.uk">c.orengo@ucl.ac.uk</a>></span><br>Date: Sun, 1 Jun 2025, 12:49<br>Subject: ELIXIR 3D-BioInfo Implementation Study application for integration of protein annotations in PDBe-KB<br>To: <a href="mailto:3d-bioinfo@elixir-europe.org">3d-bioinfo@elixir-europe.org</a> <<a href="mailto:3d-bioinfo@elixir-europe.org">3d-bioinfo@elixir-europe.org</a>><br>Cc: Sameer Velankar <<a href="mailto:sameer@ebi.ac.uk">sameer@ebi.ac.uk</a>>, Jennifer Fleming <<a href="mailto:jfleming@ebi.ac.uk">jfleming@ebi.ac.uk</a>>, R. Gonzalo Parra <<a href="mailto:gonzalo.parra@bsc.es">gonzalo.parra@bsc.es</a>>, Vincent Zoete <vincent.zoete@sib.swiss>, <a href="mailto:arne.elofsson@gmail.com">arne.elofsson@gmail.com</a> <<a href="mailto:arne.elofsson@gmail.com">arne.elofsson@gmail.com</a>>, Bohdan Schneider <<a href="mailto:bohdan@ibt.cas.cz">bohdan@ibt.cas.cz</a>><br></div><br><br>
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Dear 3D-BioInfo Community</div>
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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.</div>
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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.</div>
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The ELIXIR call for these studies is now live and 3D-BioInfo will be applying. </div>
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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). </div>
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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. </div>
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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.</div>
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Expression of Interest (EOI) for Implementation Study Funding</div>
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<u><a href="https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7" id="m_1902650181963410470OWA79314e45-3c02-ece3-5d3f-39f6a30da2ce" title="Original URL: https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7. Click or tap if you trust this link." style="color:rgb(150,96,125)" target="_blank" rel="noreferrer">https://docs.google.com/document/d/1D7_p8CM832yK8HmZ3LKhceXhbCWcc20nP9o31-zgj70/edit?tab=t.0#heading=h.30rc0e6z3ov7</a></u></div>
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Background</div>
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<u><a href="https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing" id="m_1902650181963410470OWA96f7ea90-c634-6de6-097b-90e940bb647a" title="Original URL: https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing. Click or tap if you trust this link." style="color:rgb(150,96,125)" target="_blank" rel="noreferrer">https://docs.google.com/document/d/1o0i_7gpAmOirDT9h8RFwMt7-TcBDHMsBYX1dvx3JE2E/edit?usp=sharing</a></u></div>
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Ideas</div>
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<u><a href="https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0" id="m_1902650181963410470OWA4fefb8e6-31f8-6225-e086-939915fe8b4c" title="Original URL: https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0. Click or tap if you trust this link." style="color:rgb(150,96,125)" target="_blank" rel="noreferrer">https://docs.google.com/document/d/1If6mTJb2_2p31BD88qgkqK6JcnwEpbLwkIwtYbBGp8w/edit?tab=t.0</a></u></div>
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Participants list:</div>
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<u><a href="https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0" id="m_1902650181963410470OWA7b9751cd-5236-3e65-b1b9-ee57b144263a" title="Original URL: https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0. Click or tap if you trust this link." style="color:rgb(150,96,125)" target="_blank" rel="noreferrer">https://docs.google.com/document/d/1SMoMb6X1Fvyn7aJ_YUaPFE19uytENUVigJ6u6AgR8s4/edit?tab=t.0</a></u></div>
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<b>Please add your name and details to the participant list in the google docs.</b></div>
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<b>We need to submit the application to the hub by June 15th</b> so please add your name by then to help increase the chance this study will be funded. </div>
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It will also be possible to join the study after that date by adding your name.</div>
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Thanks very much</div>
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Christine</div>
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On behalf of 3D-BioInfo coordinating team</div>
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Sameer Velankar, Arne Elofsson, Vincent Zoete, Bohdan Schneider, Gonzalo Parra</div>
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