Sat 6:30 a.m. - 6:35 a.m.
|
Opening Remarks
(
Remarks
)
>
SlidesLive Video
|
🔗
|
Sat 6:35 a.m. - 7:00 a.m.
|
Invited Speaker
(
Talk
)
>
SlidesLive Video
|
David Fleet
🔗
|
Sat 7:00 a.m. - 7:15 a.m.
|
Latent Space Diffusion Models of Cryo-EM Structures
(
Oral
)
>
SlidesLive Video
|
Karsten Kreis · Tim Dockhorn · Zihao Li · Ellen Zhong
🔗
|
Sat 7:15 a.m. - 7:30 a.m.
|
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
(
Oral
)
>
SlidesLive Video
|
Namrata Anand · Tudor Achim
🔗
|
Sat 7:30 a.m. - 7:45 a.m.
|
Predicting conformational landscapes of known and putative fold-switching proteins using AlphaFold2
(
Oral
)
>
SlidesLive Video
|
Hannah Wayment-Steele · Sergey Ovchinnikov · Lucy Colwell · Dorothee Kern
🔗
|
Sat 7:45 a.m. - 8:05 a.m.
|
Break
|
🔗
|
Sat 8:05 a.m. - 8:30 a.m.
|
Invited Speaker
(
Talk
)
>
SlidesLive Video
|
🔗
|
Sat 8:30 a.m. - 8:45 a.m.
|
SWAMPNN: End-to-end protein structures alignment
(
Oral
)
>
SlidesLive Video
|
Jeanne Trinquier · Samantha Petti · Shihao Feng · Johannes Soeding · Martin Steinegger · Sergey Ovchinnikov
🔗
|
Sat 8:45 a.m. - 9:00 a.m.
|
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
(
Oral
)
>
SlidesLive Video
|
Gabriele Corso · Hannes Stärk · Bowen Jing · Regina Barzilay · Tommi Jaakkola
🔗
|
Sat 9:00 a.m. - 9:15 a.m.
|
Dynamic-backbone protein-ligand structure prediction with multiscale generative diffusion models
(
Oral
)
>
SlidesLive Video
|
Zhuoran Qiao · Weili Nie · Arash Vahdat · Thomas Miller · Anima Anandkumar
🔗
|
Sat 9:15 a.m. - 10:15 a.m.
|
Poster Session
(
Poster Session
)
>
|
🔗
|
Sat 10:15 a.m. - 11:00 a.m.
|
Lunch
|
🔗
|
Sat 11:00 a.m. - 11:25 a.m.
|
Invited Speaker
(
Talk
)
>
SlidesLive Video
|
Max Welling
🔗
|
Sat 11:25 a.m. - 11:40 a.m.
|
EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
(
Oral
)
>
SlidesLive Video
|
Jae Hyeon Lee · Payman Yadollahpour · Andrew Watkins · Nathan Frey · Andrew Leaver-Fay · Stephen Ra · Vladimir Gligorijevic · Kyunghyun Cho · Aviv Regev · Richard Bonneau
🔗
|
Sat 11:40 a.m. - 11:55 a.m.
|
Predicting Ligand – RNA Binding Using E3-Equivariant Network and Pretraining
(
Oral
)
>
SlidesLive Video
|
Zhenfeng Deng · Ruichu Gu · Hangrui Bi · Xinyan Wang · Zhaolei Zhang · Han Wen
🔗
|
Sat 11:55 a.m. - 12:20 p.m.
|
Invited Speaker
(
Talk
)
>
SlidesLive Video
|
Alex Rives
🔗
|
Sat 12:20 p.m. - 12:35 p.m.
|
Seq2MSA: A Language Model for Protein Sequence Diversification
(
Oral
)
>
SlidesLive Video
|
Pascal Sturmfels · Roshan Rao · Robert Verkuil · Zeming Lin · Tom Sercu · Adam Lerer · Alex Rives
🔗
|
Sat 12:35 p.m. - 12:50 p.m.
|
Metal3D: Accurate prediction of transition metal ion location via deep learning
(
Oral
)
>
SlidesLive Video
|
Simon Dürr
🔗
|
Sat 12:50 p.m. - 1:50 p.m.
|
Panel Session
(
Discussion Panel
)
>
SlidesLive Video
|
🔗
|
Sat 1:50 p.m. - 2:55 p.m.
|
Poster Session / Happy Hour
(
Poster Session
)
>
|
🔗
|
Sat 2:55 p.m. - 3:00 p.m.
|
Closing Remarks
(
Remarks
)
>
SlidesLive Video
|
🔗
|
-
|
Identifying endogenous peptide receptors by combining structure and transmembrane topology prediction
(
Poster
)
>
|
Felix Teufel · Jan Christian Refsgaard · Christian Toft Madsen · Carsten Stahlhut · Mads Grønborg · Dennis Madsen · Ole Winther
🔗
|
-
|
Designing Biological Sequences via Meta-Reinforcement Learning and Bayesian Optimization
(
Poster
)
>
|
Leo Feng · Padideh Nouri · Aneri Muni · Yoshua Bengio · Pierre-Luc Bacon
🔗
|
-
|
Agile Language Transformers for Recombinant Protein Expression Optimization
(
Poster
)
>
|
Jeliazko Jeliazkov · Maxim Shapovalov · Diego del Alamo · Matt Sternke · Joel Karpiak
🔗
|
-
|
ModelAngelo: Automated Model Building in Cryo-EM Maps
(
Poster
)
>
|
Kiarash Jamali · Dari Kimanius · Sjors Scheres
🔗
|
-
|
Unsupervised language models for disease variant prediction
(
Poster
)
>
|
Allan Zhou · Nicholas C. Landolfi · Daniel ONeill
🔗
|
-
|
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem
(
Poster
)
>
|
Jason Yim · Brian L Trippe · Doug Tischer · David Baker · Tamara Broderick · Regina Barzilay · Tommi Jaakkola
🔗
|
-
|
Online Inference of Structure Factor Amplitudes for Serial X-ray Crystallography
(
Poster
)
>
|
Kevin Dalton · Doeke Hekstra
🔗
|
-
|
Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness
(
Poster
)
>
|
33 presenters
Sharrol Bachas · Goran Rakocevic · David Spencer · Anand Sastry · Robel Haile · John Sutton · George Kasun · Andrew Stachyra · Jahir Gutierrez · Edriss Yassine · Borka Medjo · Vincent Blay · Christa Kohnert · Jennifer Stanton · Alexander Brown · Nebojsa Tijanic · Cailen McCloskey · Rebecca Viazzo · Rebecca Consbruck · Hayley Carter · Simon Gottreich-Levine · Shaheed Abdulhaqq · Jacob Shaul · Abigail Ventura · Randal Olson · Engin Yapici · Joshua Meier · Sean McClain · Matthew Weinstock · Gregory Hannum · Ariel Schwartz · Miles Gander · Roberto Spreafico
🔗
|
-
|
Fast and Accurate Antibody Structure Prediction without Sequence Homologs
(
Poster
)
>
SlidesLive Video
|
Jiaxiang Wu · Fandi Wu · Biaobin Jiang · Wei Liu · Peilin Zhao
🔗
|
-
|
ExpressUrself: A spatial model for predicting recombinant expression from mRNA sequence
(
Poster
)
>
SlidesLive Video
|
Michael P Dunne · Javier Caceres-Delpiano
🔗
|
-
|
Adversarial Attacks on Protein Language Models
(
Poster
)
>
SlidesLive Video
|
Ginevra Carbone · Francesca Cuturello · Luca Bortolussi · Alberto Cazzaniga
🔗
|
-
|
The geometry of hidden representations of protein language models
(
Poster
)
>
SlidesLive Video
|
Lucrezia Valeriani · Francesca Cuturello · Alessio Ansuini · Alberto Cazzaniga
🔗
|
-
|
Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction
(
Poster
)
>
|
Shuo Zhang · Lei Xie · Yang Liu
🔗
|
-
|
Improving Molecule Properties Through 2-Stage VAE
(
Poster
)
>
|
Chenghui Zhou · Barnabas Poczos
🔗
|
-
|
Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures
(
Poster
)
>
|
Carmen Al Masri · Francesco Trozzi · Marcel Patek · Anna Cichonska · Balaguru Ravikumar · Rayees Rahman
🔗
|
-
|
Heterogeneous reconstruction of deformable atomic models in Cryo-EM
(
Poster
)
>
|
Youssef Nashed · Ariana Peck · Julien Martel · Axel Levy · Bongjin Koo · Gordon Wetzstein · Nina Miolane · Daniel Ratner · Frederic Poitevin
🔗
|
-
|
Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks
(
Poster
)
>
SlidesLive Video
|
Geoffroy Dubourg-Felonneau · Arash Abbasi · Eyal Akiva · Lawrence Lee
🔗
|
-
|
EvoOpt: an MSA-guided, fully unsupervised sequence optimization pipeline for protein design
(
Poster
)
>
|
Hideki Yamaguchi · Yutaka Saito
🔗
|
-
|
ChemSpacE: Interpretable and Interactive Chemical Space Exploration
(
Poster
)
>
|
Yuanqi Du · Xian Liu · Nilay Shah · Shengchao Liu · Jieyu Zhang · Bolei Zhou
🔗
|
-
|
T-cell receptor specific protein language model for prediction and interpretation of epitope binding (ProtLM.TCR)
(
Poster
)
>
|
Ahmed Essaghir
🔗
|
-
|
Representation Learning on Biomolecular Structures using Equivariant Graph Attention
(
Poster
)
>
SlidesLive Video
|
Tuan Le · Frank Noe · Djork-Arné Clevert
🔗
|
-
|
What is hidden in the darkness? Characterization of AlphaFold structural space
(
Poster
)
>
|
Janani Durairaj · Joana Maria Soa Pereira · Mehmet Akdel · Torsten Schwede
🔗
|
-
|
So ManyFolds, So Little Time: Efficient Protein Structure Prediction With pLMs and MSAs
(
Poster
)
>
SlidesLive Video
|
Thomas D Barrett · Amelia Villegas-Morcillo · Louis Robinson · Benoit Gaujac · Karim Beguir · Arthur Flajolet
🔗
|
-
|
Peptide-MHC Structure Prediction With Mixed Residue and Atom Graph Neural Network
(
Poster
)
>
SlidesLive Video
|
13 presenters
Antoine Delaunay · Yunguan Fu · Alberto Bégué · Robert McHardy · Bachir Djermani · Liviu Copoiu · Michael Rooney · Andrey Tovchigrechko · Marcin Skwark · Nicolas Lopez Carranza · Maren Lang · Karim Beguir · Ugur Sahin
🔗
|
-
|
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
(
Poster
)
>
|
Matan Halfon · Dina Schneidman · Tomer Cohen · raanan fattal
🔗
|
-
|
End-to-end accurate and high-throughput modeling of antibody-antigen complexes
(
Poster
)
>
|
Tomer Cohen · Dina Schneidman
🔗
|
-
|
Deep Local Analysis estimates effects of mutations on protein-protein interactions
(
Poster
)
>
|
Yasser Mohseni Behbahani · Elodie Laine · Alessandra Carbone
🔗
|
-
|
Membrane and microtubule rapid instance segmentation with dimensionless instance segmentation by learning graph representations of point clouds
(
Poster
)
>
SlidesLive Video
|
Robert Kiewisz · Tristan Bepler
🔗
|
-
|
Masked inverse folding with sequence transfer for protein representation learning
(
Poster
)
>
SlidesLive Video
|
Kevin Yang · Niccoló Zanichelli · Hugh Yeh
🔗
|
-
|
3D Reconstruction of Protein Complex Structures Using Synthesized Multi-View AFM Images
(
Poster
)
>
SlidesLive Video
|
Jaydeep Rade · Soumik Sarkar · Anwesha Sarkar · Adarsh Krishnamurthy
🔗
|
-
|
Protein structure generation via folding diffusion
(
Poster
)
>
SlidesLive Video
|
Kevin Wu · Kevin Yang · Rianne van den Berg · James Zou · Alex X Lu · Ava Soleimany
🔗
|
-
|
Learning Free Energy Pathways through Reinforcement Learning of Adaptive Steered Molecular Dynamics
(
Poster
)
>
|
Nicholas Ho · John Kevin Cava · John Vant · Ankita Shukla · Jacob Miratsky · Pavan Turaga · Ross Maciejewski · Abhishek Singharoy
🔗
|
-
|
Representation of missense variants for predicting modes of action
(
Poster
)
>
SlidesLive Video
|
Guojie Zhong · Yufeng Shen
🔗
|
-
|
Pretrained protein language model transfer learning: is the final layer representation what we want?
(
Poster
)
>
SlidesLive Video
|
Francesca-Zhoufan Li · Ava Soleimany · Kevin Yang · Alex X Lu
🔗
|
-
|
Does Inter-Protein Contact Prediction Benefit from Multi-Modal Data and Auxiliary Tasks?
(
Poster
)
>
|
Arghamitra Talukder · Rujie Yin · Yang Shen · Yuning You
🔗
|
-
|
Conditional Invariances for Conformer Invariant Protein Representations
(
Poster
)
>
|
Balasubramaniam Srinivasan · Vassilis Ioannidis · Soji Adeshina · Mayank Kakodkar · George Karypis · Bruno Ribeiro
🔗
|
-
|
Investigating graph neural network for RNA structural embedding
(
Poster
)
>
|
vaitea opuu · Helene Bret
🔗
|
-
|
Explainable Deep Generative Models, Ancestral Fragments, and Murky Regions of the Protein Structure Universe
(
Poster
)
>
|
Eli Draizen · Cameron Mura · Philip Bourne
🔗
|
-
|
APPRAISE: ranking engineered proteins by target binding propensity using pair-wise, competitive structure modeling and physics-informed analysis
(
Poster
)
>
|
Xiaozhe Ding · Xinhong Chen · Erin Sullivan · Tim Miles · Viviana Gradinaru
🔗
|
-
|
Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC
(
Poster
)
>
|
Patrick Emami · Aidan Perreault · Jeffrey Law · David Biagioni · Peter St. John
🔗
|
-
|
Training self-supervised peptide sequence models on artificially chopped proteins
(
Poster
)
>
SlidesLive Video
|
Gil Sadeh · Zichen Wang · Jasleen Grewal · Huzefa Rangwala · Layne Price
🔗
|
-
|
Protein Sequence Design in a Latent Space via Model-based Reinforcement Learning
(
Poster
)
>
SlidesLive Video
|
Minji Lee · Luiz Felipe Vecchietti · Hyunkyu Jung · Hyunjoo Ro · Ho Min Kim · Meeyoung Cha
🔗
|
-
|
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space
(
Poster
)
>
|
Gian Marco Visani · Michael Pun · Armita Nourmohammad
🔗
|
-
|
Protein-Protein Docking with Iterative Transformer
(
Poster
)
>
|
Lee-Shin Chu · Jeffrey Ruffolo · Jeffrey Gray
🔗
|
-
|
Structure-based Drug Design with Equivariant Diffusion Models
(
Poster
)
>
|
12 presenters
Arne Schneuing · Yuanqi Du · Charles Harris · Arian Jamasb · Ilia Igashov · weitao Du · Tom Blundell · Pietro Lió · Carla Gomes · Max Welling · Michael Bronstein · Bruno Correia
🔗
|
-
|
Reconstruction of polymer structures from contact maps with Deep Learning
(
Poster
)
>
SlidesLive Video
|
Atreya Dey
🔗
|
-
|
Contrasting drugs from decoys
(
Poster
)
>
SlidesLive Video
|
Samuel Sledzieski · Rohit Singh · Lenore J Cowen · Bonnie Berger
🔗
|
-
|
Learning from physics-based features improves protein property prediction
(
Poster
)
>
SlidesLive Video
|
Amy Wang · Ava Soleimany · Alex X Lu · Kevin Yang
🔗
|
-
|
RL Boltzmann Generators for Conformer Generation in Data-Sparse Environments
(
Poster
)
>
|
Yash Patel · Ambuj Tewari
🔗
|
-
|
3D alignment of cryogenic electron microscopy density maps by minimizing their Wasserstein distance
(
Poster
)
>
SlidesLive Video
|
Aryan Tajmir Riahi · Geoffrey Woollard · Frederic Poitevin · Anne Condon · Khanh Dao Duc
🔗
|
-
|
A Benchmark Framework for Evaluating Structure-to-Sequence Models for Protein Design
(
Poster
)
>
SlidesLive Video
|
Jeffrey Chan · Seyone Chithrananda · David Brookes · Sam Sinai
🔗
|
-
|
Predicting Immune Escape with Pretrained Protein Language Model Embeddings
(
Poster
)
>
SlidesLive Video
|
Kyle Swanson · Howard Chang · James Zou
🔗
|
-
|
Visualizing DNA reaction trajectories with deep graph embedding approaches
(
Poster
)
>
|
Chenwei Zhang · Anne Condon · Khanh Dao Duc
🔗
|
-
|
MLPfold: Identification of transition state ensembles in molecular dynamics simulations using machine learning
(
Poster
)
>
|
Preetham Venkatesh
🔗
|
-
|
Predicting interaction partners using masked language modeling
(
Poster
)
>
|
Damiano Sgarbossa · Umberto Lupo · Anne-Florence Bitbol
🔗
|
-
|
ZymCTRL: a conditional language model for the controllable generation of artificial enzymes
(
Poster
)
>
|
Noelia Ferruz
🔗
|
-
|
Large-scale self-supervised pre-training on protein three-dimensional structures
(
Poster
)
>
SlidesLive Video
|
Ilya Senatorov
🔗
|
-
|
Fast protein structure searching using structure graph embeddings
(
Poster
)
>
|
Joe Greener · Kiarash Jamali
🔗
|
-
|
A Federated Learning benchmark for Drug-Target Interaction
(
Poster
)
>
|
Filip Svoboda · Gianluca Mittone · Nicholas Lane · Pietro Lió
🔗
|
-
|
Physics aware inference for the cryo-EM inverse problem: anisotropic network model heterogeneity, global 3D pose and microscope defocus
(
Poster
)
>
|
Geoffrey Woollard · Shayan Shekarforoush · Frank Wood · Marcus Brubaker · Khanh Dao Duc
🔗
|
-
|
Allele-conditional attention mechanism for HLA-peptide complex binding affinity prediction
(
Poster
)
>
SlidesLive Video
|
Rodrigo Hormazabal · Doyeong Hwang · Kiyoung Kim · Sehui Han · Kyunghoon Bae · Honglak Lee
🔗
|
-
|
Conditional neural processes for molecules
(
Poster
)
>
|
Miguel Garcia-Ortegon · Andreas Bender · Sergio Bacallado
🔗
|
-
|
Towards automated crystallographic structure refinement with a differentiable pipeline
(
Poster
)
>
|
Minhuan Li · Doeke Hekstra
🔗
|
-
|
Ligand-aware protein sequence design using protein self contacts
(
Poster
)
>
|
Jody Mou · Benjamin Fry · Chun-Chen Yao · Nicholas Polizzi
🔗
|
-
|
Lightweight Equivariant Graph Representation Learning for Protein Engineering
(
Poster
)
>
SlidesLive Video
|
Bingxin Zhou · · Kai Yi · Xinye Xiong · Pan Tan · Liang Hong · Yuguang Wang
🔗
|
-
|
Improving Molecular Pretraining with Complementary Featurizations
(
Poster
)
>
|
Yanqiao Zhu · Dingshuo Chen · Yuanqi Du · Yingze Wang · Qiang Liu · Shu Wu
🔗
|
-
|
Using domain-domain interactions to probe the limitations of MSA pairing strategies
(
Poster
)
>
|
Alex Hawkins-Hooker · David Jones · Brooks Paige
🔗
|
-
|
Metal3D: Accurate prediction of transition metal ion location via deep learning
(
Poster
)
>
SlidesLive Video
|
Simon Dürr
🔗
|
-
|
Predicting conformational landscapes of known and putative fold-switching proteins using AlphaFold2
(
Poster
)
>
SlidesLive Video
|
Hannah Wayment-Steele · Sergey Ovchinnikov · Lucy Colwell · Dorothee Kern
🔗
|
-
|
Dynamic-backbone protein-ligand structure prediction with multiscale generative diffusion models
(
Poster
)
>
SlidesLive Video
|
Zhuoran Qiao · Weili Nie · Arash Vahdat · Thomas Miller · Anima Anandkumar
🔗
|
-
|
Predicting Ligand – RNA Binding Using E3-Equivariant Network and Pretraining
(
Poster
)
>
SlidesLive Video
|
Zhenfeng Deng · Ruichu Gu · Hangrui Bi · Xinyan Wang · Zhaolei Zhang · Han Wen
🔗
|
-
|
Seq2MSA: A Language Model for Protein Sequence Diversification
(
Poster
)
>
|
Pascal Sturmfels · Roshan Rao · Robert Verkuil · Zeming Lin · Tom Sercu · Adam Lerer · Alex Rives
🔗
|
-
|
EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
(
Poster
)
>
|
Jae Hyeon Lee · Payman Yadollahpour · Andrew Watkins · Nathan Frey · Andrew Leaver-Fay · Stephen Ra · Vladimir Gligorijevic · Kyunghyun Cho · Aviv Regev · Richard Bonneau
🔗
|
-
|
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
(
Poster
)
>
SlidesLive Video
|
Gabriele Corso · Hannes Stärk · Bowen Jing · Regina Barzilay · Tommi Jaakkola
🔗
|
-
|
SWAMPNN: End-to-end protein structures alignment
(
Poster
)
>
SlidesLive Video
|
Jeanne Trinquier · Samantha Petti · Shihao Feng · Johannes Soeding · Martin Steinegger · Sergey Ovchinnikov
🔗
|
-
|
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
(
Poster
)
>
|
Namrata Anand · Tudor Achim
🔗
|
-
|
Latent Space Diffusion Models of Cryo-EM Structures
(
Poster
)
>
|
Karsten Kreis · Tim Dockhorn · Zihao Li · Ellen Zhong
🔗
|