Charlotte Deane
University of Oxford
UK
EMBO Workshop
This conference will take place at EMBL Heidelberg, with the option to attend virtually.
The field of computational structural biology is undergoing a revolution. AlphaFold, a program based on Artificial Intelligence (AI), has transformed the structural modeling of proteins and protein complexes by reaching accuracy similar to experimental structures. Over 200 million structural models have already been released in AlphaFold Database. Following AlphaFold, other protein modeling programs proliferated from researchers worldwide. AI has started advancing RNA modeling too. The wealth of protein models has sparked an explosion of new tools for structural analysis and structure-based function assignment. Scientists from other fields, such as system biology, incorporate AI-based structure prediction in their pipelines. In parallel, molecular dynamics simulations push the limits of accuracy and size of what can be simulated. Protein and drug design are being transformed thanks to new geometric AI methods and the availability of structural models for almost any drug target.
With this “Cambrian explosion” of computational structural biology, this event aims to become a so-far missing major dedicated conference. Our conference will update on the impact of AI-based structure prediction, provide a forum to present new methods and applications, build a wider community by integrating the new scientists now massively joining the field, and open a platform to discuss future directions and opportunities.
Please see EMBL’s COVID-19 safety recommendations if attending the on-site event.
University of Oxford
UK
University of Illinois at Urbana-Champaign
USA
University of Queensland
Australia
Seoul National University
South Korea
University of Washington
USA
(Virtual speaker)
ETH Zürich
Switzerland
Utrecht University
THe Netherlands
International Institute of Molecular and Cell Biology in Warsaw
Poland
Stockholm University
Sweden
DeepMind
UK
Małopolska Centre of Biotechnology UJ
Poland
Sorbonne Université
France
University of Bristol
UK
Max Planck Institute of Biophysics
Germany
University of California Riverside
USA
Technical University of Berlin
Germany
University of California, San Francisco
USA
Hebrew University of Jerusalem
Israel
(Virtual speaker)
Seoul National University
South Korea
(Virtual speaker)
RIKEN Cluster for Pioneering Research
Japan
University of California, San Diego
USA
EMBL Hamburg
Germany
University College London
UK
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Time (Europe/Berlin) | Session |
---|---|
11:30 – 13:00 | Registration and light refreshments |
13:00 – 13:10 | Opening remarks |
Session 1: Modeling proteins and nucleic acids Session Chair: Sameer Velankar – EMBL-EBI, UK | |
13:10 – 13:40 | Building on AlphaFold John Jumper – Google DeepMind, UK |
13:40 – 14:10 | Protein Structure and Interaction Prediction using RoseTTAFold Minkyung Baek – Seoul National University, Republic of Korea |
14:10 – 14:25 | Cryo-OrbiSIMS enables accurate 3D modelling of native RNA structures at atomic resolution Aditi Borkar – University of Nottingham, United Kingdom VIRTUAL TALK |
14:25 – 14:40 | Integrating physics in deep learning algorithms: a force field as a PyTorch module Gabriele Orlando – KU Leuven, Belgium |
14:40 – 15:10 | Searching the molecular spaces using neural network energy models Chaok Seok – Seoul National University, South Korea Not available on demand VIRTUAL TALK |
15:10 – 15:40 | Computational modeling of RNA 3D structures and interactions – with and without the use of experimental data Janusz Bujnicki – International Institute of Molecular and Cell Biology in Warsaw, Poland |
15:40 – 16:10 | Coffee Break + Meet the speakers |
Session 2: Modeling complexes Session Chair: Zoe Cournia – Biomedical Research Foundation of the Academy of Athens, Greece | |
16:10 – 16:40 | Towards a complete structural map of the human proteome using AlphaFold Arne Elofsson – Stockholm University, Sweden |
16:40 – 17:10 | Modeling protein-peptide complexes Ora Schueler-Furman – The Hebrew University of Jerusalem, Israel VIRTUAL TALK |
17:10 – 17:25 | Biophysics-aware machine learning models for pMHC-TCR binding prediction Martin Culka – Columbia University, USA |
17:25 – 17:40 | End-to-end deep learning model for accurate and high-throughput prediction of antibody-antigen complexes Dina Schneidman – The Hebrew University of Jerusalem, Israel |
17:40 – 17:55 | Pairing interacting protein sequences using masked language modeling Damiano Sgarbossa – EPFL, Switzerland |
17:55 – 18:25 | Structural modeling of nuclear pore complexes Agnieszka Obarska-Kosinska – Max Planck Institute of Biophysics, Germany |
18:25 – 20:00 | Dinner at EMBL Canteen |
20:00 – 22:00 | Pub Quiz and drinks in Canteen |
Time (Europe/Berlin) | Session |
---|---|
Session 3: Structural dynamics Session Chair: Rommie Amaro – University of California, San Diego, USA | |
09:00 – 09:30 | In Situ Computational Microscopy of SARS/CoV2 Rommie Amaro – University of California, San Diego, USA |
09:30 – 09:45 | Multiscale computer simulations reveal the role of membrane, protein and water dynamics in energy production in mitochondria Vivek Sharma – University of Helsinki, Finland |
09:45 – 10:00 | Dissecting the structural basis behind higher specificity of FnCas9 protein Gayatri Panda – Indraprastha Institute of Information Technology, India |
10:00 – 10:30 | Multiscale Simulation for Drug resistance, Enzyme Design and Evolution Adrian Mulholland – University of Bristol, UK |
10:30 – 11:00 | Coffee Break + Meet the speakers + Meet the Editors |
11:00 – 11:15 | Computing residence time and investigating dissociation mechanisms of protein-protein interactions Giulia D’Arrigo – Heidelberg Institute for Theoretical Studies (HITS), Germany |
11:15 – 11:30 | Integrative modelling of glycans in the SARS-CoV-2 spike protein and beyond Mateusz Sikora – Jagiellonian University, Poland |
11:30 – 12:00 | The monomeric structures of GRB2 in solution by integrated modeling Yuji Sugita – RIKEN, Japan |
12:00 – 12:30 | Flash talks #55 Barone, Federico #73 de Vries, Ida #97 Loison, Claire #99 Hori, Naoto #107 Justyna, Marek #135 Mukherjee, Sunandan #141 Paladino, Antonella #149 Rinaldi, Francesco #159 Shor, Ben #165 Srivastava, Mitul #171 Talagayev, Valerij |
12:30 – 14:00 | Lunch, meet the speakers and job fair |
14:00 – 15:00 | Poster Session 1 (odd numbers) View poster listing here |
15:00 – 15:30 | Coffee Break and Meet the speakers and ERC Session “ERC funding opportunities” |
Session 4: Structure-based function assignment and analysis Session Chair: Christine Orengo ‑ University College London, UK | |
15:30 – 16:00 | Computational Enzymology: towards using knowledge of structure and function to identify paradigms of evolution and to predict enzyme mechanisms. Janet Thornton – EMBL-EBI, UK |
16:00 – 16:15 | The geometry of hidden representations of protein language models Alberto Cazzaniga – AREA Science Park, Italy |
16:15 – 16:30 | Towards the design of targeted therapeutics based on microbial and antimicrobial amyloids Peleg Ragonis-Bachar – Technion – Israel institute of Technology, Israel |
16:30 – 17:00 | Applications of the new AI-based modeling methods to annotate function of microbial proteins on an evolutionary scale Tomasz Kosciołek – Jagiellonian University, & Silesian University of Technology, Poland |
17:00 – 17:15 | Dissecting the sequence and structure determinants of gpcr-gprotein selectivity via structural bioinformatics and machine learning Marin Matic – Scuola Normale Superiore, Italy |
17:15 – 17:45 | The impact of sequence variations on protein interactions and motions Elodie Laine – Sorbonne Université, France |
17:45 | Free afternoon |
Time (Europe/Berlin) | Session |
---|---|
Session 5: Structural bioinformatics and experiments Session Chair: Jan Kosinski – EMBL Hamburg, Germany | |
09:00 – 09:45 | Keynote lecture: Can machine learning understand the physics of binding? Charlotte Deane – University of Oxford, UK |
09:45 – 10:15 | Towards accurate antibody-antigen complex prediction from sequence using AI and integrative modelling Alexandre Bonvin – Utrecht University, The Netherlands |
10:15 – 10:45 | Localizing intrinsically disordered regions of proteins in integrative structures of large macromolecular assemblies Shruthi Viswanath – Tata Institute of Fundamental Research, India Not available on demand |
10:45 – 11:30 | Coffee Break + Meet the speakers |
11:30 – 11:45 | Structure determination of an eIF2 dephosphorylation complex that terminates signalling in the integrated stress response Yahui Yan – University of Cambridge, United Kingdom |
11:45 – 12:15 | Visualising protein complexes inside cells Juri Rappsilber – Technische Universität Berlin, Germany |
12:15 – 12:30 | Inferring residue level hydrogen deuterium exchange with ReX Oliver Crook – University of Oxford, United Kingdom |
12:30 – 12:45 | Enhanced modeling of water molecules in dynamic Protein-Ligand structures Stephanie Wankowicz – University of California, San Francisco, USA |
12:45 – 13:15 | Flash talks #62 Brandner, Astrid #64 Bryant, Patrick #78 Duman, Özge #82 Parra, R. Gonzalo #94 Haddad Bassam #100 Jalalypour, Farzaneh #134 Molodenskiy, Dmitry #170 Surpeta, Bartlomiej #184 Wirnsberger, Gregor |
13:15 – 14:45 | Lunch, meet the speakers and job fair |
14:45 – 16:15 | Poster Session 2 (even numbers) View poster listing here |
Session 6: Applications: drugs, protein design, and more Session Chair: Katja Luck ‑ Institute of Molecular Biology, Mainz, Germany | |
16:15 – 16:45 | Applications of computational methods to predict effects of disease-related mutations and design drug molecules David Ascher – University of Queensland, Australia |
16:45 – 17:00 | Predicting protein-membrane interfaces using molecular simulations and ensemble machine learning Zoe Cournia – Biomedical Research Foundation Academy of Athens, Greece Not available on demand |
17:00 – 17:30 | Coffee Break + Meet the speakers |
17:30 – 17:45 | Reality check – evaluating generative models for protein and ligand design Charlie Harris – University of Cambridge, United Kingdom |
17:45 – 18:00 | Identification of HIV broadly neutralizing antibodies using a Deep Language Model Chiara Rodella – University of Bern, Switzerland |
18:00 – 18:30 | Design of new protein functions using deep learning David Baker – University of Washington, USA VIRTUAL TALK |
18:30 – 20:30 | Dinner at EMBL Canteen |
20:30 – 00:00 | Conference party with DJ |
Time (Europe/Berlin) | Session |
---|---|
Session 7: Structural systems biology Session Chair: Edward Marcotte – The University of Texas at Austin, USA | |
09:30 – 10:15 | Keynote lecture: 4D simulations of a growing minimal cell Zaida (Zan) Luthey-Schulten – University of Illinois at Urbana-Champaign, USA |
10:15 – 10:45 | From integrative structural biology to cell biology Andrej Sali – University of California, San Francisco, USA |
10:45 – 11:00 | Interactions of pathogen metabolic and virulence processes revealed through deep learning and coevolution Ian Humphreys – University of Washington, USA |
11:00 – 11:30 | Coffee Break + Meet the speakers |
11:30 – 11:45 | Combining AI structure prediction, mass spectrometry, and cryo-EM to unlock the mysteries of motile cilia Caitlyn McCafferty – University of Basel, Switzerland |
11:45 – 12:15 | Structure-guided prediction of mechanistic impacts of human protein missense variants Pedro Beltrao – ETH Zürich, Switzerland |
12:15 – 13:00 | Round-table discussion: The future of computational structural biology Janet Thornton, Giulia Palermo, Pedro Beltrao, Andrej Sali |
13:00 – 13:15 | Closing Remarks and Poster Prize |
13:15 – 13:45 | Packed Lunch and departure |
On-site registration fees include admission, conference materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses.
Virtual registration fees include access to all of the talks (livestreamed and on demand) and facility to submit questions.
On-site Academia | €450 |
On-site PhD Student | €350 |
On-site Industry | €750 |
Virtual Academia | €200 |
Virtual PhD Student | €150 |
Virtual Industry | €250 |
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On-site participants
You may apply for financial assistance when submitting your abstract. In your application you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.
Virtual participants
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As further changes in our events are possible, you should book flights, trains and hotels with flexible options and favourable cancellation conditions.
The hotels below have rooms on hold for participants until 8 November 2023, in some cases at special rates. Please email the hotel directly, quoting the booking code CSB23-01 to confirm the exact price of the room.
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Conference shuttle bus schedule
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Address: EMBL, Meyerhofstraße 1, 69117 Heidelberg, Germany. For further information on getting to EMBL Heidelberg visit Public Transportation to the Venue. For information about accommodation and local transportation please refer to the FAQ page.
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Hello | Hallo |
Goodbye | Auf Wiedersehen (formal) Tschüss (informal) |
Good morning | Guten Morgen |
Good afternoon | Guten Tag |
Good evening | Guten Abend |
Good night | Gute Nacht |
I’m sorry | Es tut mir leid |
Excuse me… | Entschuldigen Sie |
How are you? | Wie gehts? |
I’m fine thanks. And you? | Mir geht es gut , danke. Und Dir/Ihnen? |
What is your name | Wie heißen Sie? (formal) Wie heißt du? (informal) |
My name is.. | Ich heiße.. |
Do you speak English | Sprechen Sie englisch? |
I don’t understand | Ich verstehe nicht |
Please speak more slowly | Können Sie bitte langsamer sprechen |
Thank you | Dankeschön |
Where is the toilet? | Wo ist die Toilette? |
Please call me a taxi | Bitte rufen Sie mir ein Taxi |
How do I get to….? | Wie komme ich zum/zur…..? |
A beer/two beers please | Ein Bier/zwei Bier bitte |
A glass of red/white wine please | Ein Glas Rot/Weisswein bitte |
The menu, please | Die Speisekarte, bitte |
Is there a local speciality? | Gibt es eine Spezialität aus dieser Gegend? |
I’m vegetarian | Ich bin Vegetarier |
It was delicious | Es war hervorragend |
The bill, please | Die Rechnung, bitte |
I have a headache | Ich habe Kopfschmerzen |
I have a sore throat | Ich habe Halsschmerzen |
My stomach hurts | Ich habe Magenschmerzen |
I’m allergic to | Ich bin allergisch gegen |
I need a doctor who speaks English | Ich brauche einen Arzt, der englisch spricht. |
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Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for participants page.
COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
Media partners
Molecular Systems Biology, an EMBO Press journal
International Union of Biochemistry and Molecular Biology
FEBS Open Bio, a FEBS Press journal
Sponsorship opportunities
We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information on sponsoring possibilities.
If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.
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Date: 6 - 9 Dec 2023
Location: EMBL Heidelberg and Virtual
Venue: EMBL Advanced Training Centre
Deadline(s):
Abstract submission: Closed
Registration (On-site): Closed
Registration (Virtual): Closed
Organisers:
Contact: Sophie Dutzi