Schedule

Sunday, September 24th, 2023

Public conference

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16:00 - 18:00

Öffentlicher Konferenzauftakt – Public conference opening (This event is open to the public)
Protein design im Zeitalter der künstlichen Intelligenz

Moderation: Clara T. Schoeder & Jens Meiler, Leipzig University, Faculty of  Medicine
Speakers: Tanja Kortemme, UCSF & Eric. S. Fischer, Dana-Faber-Institute / Harvard Medical School

Location: Bibliotheca Albertina, Beethoven Str. 6, 04107 Leipzig, Vortragssaal im Erdgeschoss

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TBA

Speakers dinner

Day 1: Monday, September 25th, 2023

Welcome and Opening Session

Chairs: Clara T. Schoeder & Jens Meiler, Leipzig University, Faculty of Medicine

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9:00

Opening ceremony – Welcome remarks
Protein design in the age of artificial intelligence

Speaker: Clara T. Schoeder & Jens Meiler, Leipzig University, Faculty of  Medicine
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9:20

New protein shapes for new functions de novo

Speaker: Tanja Kortemme, UCSF

Session I: Protein design

Chair: Simon Kretschmer, UCSF

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10:30

Exploring new sequence space with protein design

Speaker: Birte Höcker, University of Bayreuth
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10:55

De novo design of a protein catalyst in a non-natural fold

Speaker: Gustav Oberdorfer, TU Graz
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11:15

Computational design of chemotactic receptor biosensors for enhancing immune cell tumor-targeting functions

Speaker: Ana Paola Rica Villarreal, EPFL
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11:30

Coffee Break

 

Session II: Design of assembling proteins

Chair: Christina Lamers, Leipzig University, Faculty of Medicine

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11:45

Exploring the protein assembly space with structural flexibility

Speaker: Alena Khmelinskaia, LMU Munich
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12:10

Protein assembly with Armadillo repeat fragments

Speaker: Wenzhao Dai, University of Zürich
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12:30

Programming proteins for sustainable material engineering in non-aqueous environments

Speaker: Sebastian Rämisch, Cambrium Bio
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12:45

Lunch Break and Poster Viewing

 

Session III: Machine learning

Chair: Julia Westermayr, Leipzig University, Faculty of Medicine

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14:00

ML prediction of biomolecules with RoseTTAFold2 and RoseTAFold-NA

Speaker: Frank DiMaio, University of Washington
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14:25

FLAb: Benchmarking deep learning methods for antibody fitness prediction

Speaker: Michael Chungyoun, Johns Hopkins University
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14:45

How are proteins encoded: Studying evolutionary codon usage in the age of artificial intelligence

Speaker: Rachel Kolodny, Haifa University
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15:05

GenScript Biotech collaborations with the AI protein design community

Speaker: Robert John Ford, GenScript
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15:20

Coffee Break

Session IV: Protein design

Chair: Clara T. Schoeder, Leipzig University, Faculty of Medicine

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15:45

Towards artificial proteins and alternative alphabets

Speaker: Klara Hluchova, Charles University Prague
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16:10

A complementarity-first approach to de novo binder design

Speaker: Mohammad ElGamacy, Uni Tübingen
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16:25

Multi-State Design of stimulus-responsive two-state hinge proteins

Speaker: Florian Praetorius, University of Washington
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16:45

Design of novel site-specific protein interactions using surface fingerprinting

Speaker: Anthony Marchand, EPFL

Keynote Lecture

Chair: Jens Meiler, Leipzig University, Faculty of Medicine

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17:00

Language models of protein sequences at the scale of evolution enable accurate structure prediction

Speaker: Alexander Rives, Evolutionary Scale
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18:00-20:00

Poster Session 

With Pizza
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20:00-22:00

Evening Reception

Wine and beer in the neighborhood atmosphere (hosted by the Destille)

 

Day 2: Tuesday, September 26th, 2023

Keynote Lecture

Chair: Amelie Stein, University of Copenhagen

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9:00

Computational approaches in targeted protein degradation

Speaker: Eric S. Fischer, Dana-Faber-Institute / Harvard Medical School

Session V:Enzymes and Ligands

Chair: Rocco Moretti, Vanderbilt University

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10:00

A high-throughput computational ecosystem for protein engineering

Speaker:  Zhongyue (John) Yang, Vanderbilt University 
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10:25

Protection of catalytic cofactors by ancestral polypeptides as a driver for the generation of novel enzymes

Speaker: Luis I. Gutierrez-Rus, Universidade de Granada
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10:45

Designing de novo metalloproteins using deep learning and evolutionary algorithms

Speaker: Simon L. Dürr, EPFL
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11:05

Protein binding dyes meet light-emitting diodes

Speaker: Horst Lechner, TU Graz
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11:20

Coffee Break

 

Session VI: Structure and Design of Membrane Proteins

Chair: Georg Künze, Leipzig University, Faculty of Medicine

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11:40

Computational design of multi-domain receptors with programmable sensing and signaling functions

Speaker: Lukas Rudden, EPFL
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12:05

Probing modelling of protein interactions with high-throughput assays

Speaker: Amelie Stein, University of Copenhagen
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12:25

Computational design of soluble analogues of integral membrane topologies

Speaker: Martin Pacesa, EPFL
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12:40

Poster Viewing

 

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13:00

Lunch Break

 

Session VII: : Early Career Researchers

Chair: Jens Meiler, Leipzig University, Faculty of Medicine 

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14:20

Property-driven molecular material design

Speaker: Julia Westermayr, Leipzig University, ScaDS.AI
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14:40

Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors

Speaker: Simon Kretschmer, UCSF
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15:00

TrkA receptor-clustering with de novo designed minibinders

Speaker: Thomas Schlichthärle, Univeristy of Washington
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15:20

Coffee Break

Session VIII: Rosetta Development Session

Chair: Rocco Moretti, Vanderbilt University & David Nannemann, Rosetta Design Group

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15:40

The philosophy and history of Rosetta code development

Speaker: Rocco Moretti, Vanderbilt University
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16:00

Machine learning models in Rosetta

Speaker: Moritz Ertelt, Leipzig University, and ScaDS.AI
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16:15

Challenges and opportunities in preventing misuse of protein design tools

Speaker: Samuel Curtis, The Future Society
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16:30

Round table discussion – The future of Rosetta code development

Moderation: David Nannemann, Rosetta Design Group & James Vasile, Open Tech Strategies

Keynote Lecture

Chair: Clara T. Schoeder, Leipzig University Faculty of Medicine

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17.00

How far are we from designing on antibody therapeutic on a computer?

Speaker: Charlotte Deane, Oxford University
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19:30-23:00

Conference Dinner

Moritzbastei, Leipzig

Day 3: Wednesday, September 27th, 2023

Keynote Lecture

Chair: Torben Schiffner, Leipzig University, Faculty of Medicine

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9:00

Defining the rules of engagement: an exploration of antibody-antigen interfaces

Speaker: Andrew Ward, Scripps Research Institute

Session IX: Vaccine and Antibody Design

Chair: Torben Schiffner, Leipzig University

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10:00

Germline-targeting vaccine design: toward eliciting made-to-order antibodies

Speaker: William R. Schief, Moderna, and Scripps Research Institute
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10:25

Computational screening with Rosetta identifies post-translationally modified self-peptides that induce T cell activation and cause hypertension

Speaker: Nathaniel Bloodworth, Vanderbilt University
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10:45

A novel high-throughput approach for the de novo generation of fully humanized single domain antibodies following camelid immunization by combining library design and artificial intelligence (AI)

Speaker: Andreas Evers, Merck
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11:00

De novo design of viral epitope mimetics with non-regular structural features 

Speaker: Karla Castro, EPFL
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11:20

Coffee Break

 

Session X: Structure prediction with and without experimental data

Chair: Kaitlyn Ledwitch, Vanderbilt University

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11:40

Integrating structural bioinformatics and deep learning protein structure prediction: Modeling of all 437 human protein kinases in the active state

Speaker: Roland Dunbrack, Fox-Chase Cancer
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12:05

Accurate modeling of antibody and T cell receptor recognition with deep learning

Speaker: Brian Pierce, University of Maryland
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12:25

Integral membrane protein structure prediction with spare paramagnetic NMR data

Speaker: Kaitlyn Ledwitch, Vanderbilt University
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12:45

A hybrid approach to map the misfolded state of a pathogenic Rhodopsin variant

Speaker: Victoria Most, Leipzig University, Faculty of Medicine
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13:00

Lunch Break

 

Session XI: Protein design and artificial intelligence

Chair: Alena Khmelinskaia, LMU Munich

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14:00

Computational design of proteins components for cellular functions

Speaker:  Bruno Correia, EPFL
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14:25

De novo hallucination of mechanostable proteins

Speaker: Lucas Milles, University of Washington
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14:45

Efficient and scalable de novo protein design using a relaxed sequence space

Speaker: Christopher Frank, TU Munich
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15:05

Towards biologics by design: AI-based virtual screening for multi-specific protein therapeutics

Speaker: Dilyana Dimova, Sanofi Aventis
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15:20

Coffee Break

Closing Session

Chairs: Clara T. Schoeder and Jens Meiler, Leipzig University, Faculty of Medicine

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15:45

AI tools for antibody engineering and protein docking

Speaker: Jeffrey J. Gray, Johns Hopkins University and RosettaCommons Co-director
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16:45

Closing remarks

Speaker: Clara T. Schoeder and Jens Meiler, Leipzig University, Faculty of Medicine