<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Aptos;
panose-1:2 11 0 4 2 2 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:12.0pt;
font-family:"Aptos",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
p.elementtoproof, li.elementtoproof, div.elementtoproof
{mso-style-name:elementtoproof;
margin:0cm;
font-size:12.0pt;
font-family:"Aptos",sans-serif;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Aptos",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;
mso-ligatures:none;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="en-NL" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">Seino A. K. Jongkees, Ph.D.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">Associate Professor</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#0089CF">AIMMS Amsterdam Institute of Molecular and Life Sciences</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><img width="302" height="51" style="width:3.1458in;height:.5312in" id="Picture_x0020_2" src="cid:image001.png@01DBC8A5.0BFEAB40" alt="Logo"><img width="160" height="50" style="width:1.6666in;height:.5208in" id="Picture_x0020_1" src="cid:image002.jpg@01DBC8A5.0BFEAB40" alt="AIMMS FESTIVAL – A festival of molecular science"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#5B5B5B">T </span><span lang="EN-US" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#5B5B5B"><a href="tel:+31657227168"><span lang="NL" style="color:#0078D7">+31
(0)6 5722 7168</span></a></span><span lang="NL" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#5B5B5B"> |
<a href="http://jongkeeslab.com/"><span style="color:#0563C1">jongkeeslab.com</span></a></span><span lang="NL" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#4472C4">
</span><span lang="NL" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#5B5B5B">| </span><span lang="EN-US" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#4472C4"><a href="mailto:s.a.k.jongkees@vu.nl"><span lang="NL" style="color:#0078D7">s.a.k.jongkees@vu.nl</span></a></span><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B">Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B">Visiting address: O|2 building</span><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#212121">
</span><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B;mso-fareast-language:EN-US">O2-03W11, de Boelelaan 1108, 1081 HZ Amsterdam<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B;mso-fareast-language:EN-US">Postal address: O2 03W11 c/o goederenontvangst, Van der Boechorststraat 3, 1081 BT Amsterdam</span><span lang="EN-GB" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div id="mail-editor-reference-message-container">
<div>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">From:
</span></b><span style="color:black">Hennig, S. (Sven) <s.hennig@vu.nl><br>
<b>Date: </b>Monday, 19 May 2025 at 09:40<br>
<b>To: </b>Beta Allgrossmann <allgrossmann.beta@vu.nl>, Jongkees, S.A.K. (Seino) <s.a.k.jongkees@vu.nl><br>
<b>Subject: </b>Scientific Guest Speaker cryoEM<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Hi all,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">@Seino: could you please forward to interested people from your network. thx.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Each year, we invite scientific cryoEM guest speakes in our Biostructural Elucidation course. This is a Bachelors course and the guest speaker is asked to give a road introduction as well as dive detailed into
a few of their research topics. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Please find the details below and I would be glad to see you there.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Cheers Sven<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
</div>
<p class="elementtoproof" style="background:white"><span style="color:black"> </span><span style="font-family:"Calibri",sans-serif;color:black">We are pleased to welcome Alisia Fadini from University of Cambridge, who will be visiting the VU and giving a seminar
primarily aimed at structural biology students.</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Date: TODAY: Monday, May 19</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Time: 13:30–15:15</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Location: NU-Theatre 9</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Alisia is currently working with the groups of Randy Read (University of Cambridge) and Mohammed AlQuraishi (Columbia University) at the cutting edge
of machine learning–driven protein structure prediction.</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Title: <b>ROCKET: an AlphaFold augmentation integrating crystallographic & cryoEM/ET data</b></span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Structural biology is in an era of dynamics and macromolecular assemblies, but turning raw experimental data into atomic models at scale remains challenging.
We introduce ROCKET: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data, with room for more! AF-based methods encode rich structural priors but lack a general mechanism for integrating arbitrary data modalities. ROCKET tackles this
by optimizing latent representations to fit experimental data at inference time, without retraining. ROCKET integrates experimental likelihood targets within AlphaFold’s differentiable prediction pipeline to optimize MSA profile features. Structure refinement
becomes a search in evolutionary space instead of Cartesian space. What does this unlock? ROCKET samples barrier-crossing conformations that standard refinement methods often fail to reach, such as ligand-induced loop rearrangements or domain shifts. </span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">The low-resolution challenge is also particularly key for emerging cryo-ET data. We find that ROCKET remains robust in this regime and extracts different
conformations from sub-tomogram averages.</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">ROCKET performs a new type of structure refinement by optimizing latent representations in evolutionary space. This unlocks possibilities for high-throughput
ligand screening, assemblies solved at low resolution, and conformational landscapes – bringing automation towards new frontiers.</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:#242424">After the seminar, there will be a
<b>borrel/drinks</b>, offering a chance to chat with the speaker in a more informal setting. Everyone is welcome!</span><o:p></o:p></p>
<p class="elementtoproof" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div id="Signature">
<p><span style="font-size:9.0pt">Dr. Sven Hennig</span><o:p></o:p></p>
<p><span style="font-size:9.0pt">Associate Professor<br>
Structural Chemical Biology<br>
Head of Crystallography</span><o:p></o:p></p>
<p><span style="font-size:9.0pt">Vrije University Amsterdam<br>
De Boelelaan 1108, O|2 04E05<br>
1081 HZ Amsterdam, Netherlands</span><o:p></o:p></p>
<p><span style="font-size:9.0pt">email: <a href="mailto:s.hennig@vu.nl">s.hennig@vu.nl</a><br>
web: svenslab.com</span><o:p></o:p></p>
<p> <o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</body>
</html>