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Workshop

Machine Learning in Structural Biology Workshop

Hannah Wayment-Steele ⋅ Roshan Rao ⋅ Ellen Zhong ⋅ Sergey Ovchinnikov ⋅ Gabriele Corso ⋅ Gina El Nesr
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Abstract

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Schedule

Timezone: America/Los_Angeles
6:30 AM
Opening Remarks
1:00 PM
Panel Session
3:00 PM
Closing Remarks
ESMFold Hallucinates Native-Like Protein Sequences
Jeliazko Jeliazkov ⋅ Diego del Alamo ⋅ Joel Karpiak
Conditioned Protein Structure Prediction
Tengyu Xie ⋅ Zilin Song ⋅ Jing Huang
Stable Online and Offline Reinforcement Learning for Antibody CDRH3 Design
Yannick Vogt ⋅ Mehdi Naouar ⋅ Maria Kalweit ⋅ Christoph Cornelius Miething ⋅ Justus Duyster ⋅ Roland Mertelsmann ⋅ Gabriel Kalweit ⋅ Joschka Boedecker
AlphaFold Distillation for Protein Design
Igor Melnyk ⋅ Aurelie Lozano ⋅ Payel Das ⋅ Vijil Chenthamarakshan
Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
Chengyue Gong ⋅ Adam Klivans ⋅ Jordan Wells ⋅ James Loy ⋅ Qiang Liu ⋅ Alex Dimakis ⋅ Daniel Diaz
Scalable Multimer Structure Prediction using Diffusion Models
Peter Pao-Huang ⋅ Bowen Jing ⋅ Dr. Bonnie Berger
Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction
Christopher Fifty ⋅ Joseph M Paggi ⋅ Ehsan Amid ⋅ Jure Leskovec ⋅ Ron Dror
Molecular Diffusion Models with Virtual Receptors
Matan Halfon ⋅ Eyal Rozenberg ⋅ Ehud Rivlin ⋅ Daniel Freedman
CESPED: a new benchmark for supervised particle pose estimation in Cryo-EM.
Ruben Sanchez Garcia ⋅ Michael Saur ⋅ Javier Vargas ⋅ Carl Poelking ⋅ Charlotte Deane
Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms
Bowen Jing ⋅ Tommi Jaakkola ⋅ Dr. Bonnie Berger
VN-EGNN: Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
Florian Sestak ⋅ Lisa Schneckenreiter ⋅ Sepp Hochreiter ⋅ Andreas Mayr ⋅ Günter Klambauer
Improved encoding of ensembles in PDBx/mmCIF
Stephanie Wankowicz ⋅ James Fraser
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing ⋅ Dr. Bonnie Berger ⋅ Tommi Jaakkola
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing ⋅ Dr. Bonnie Berger ⋅ Tommi Jaakkola
The Discovery of Binding Modes Requires Rethinking Docking Generalization
Gabriele Corso ⋅ Arthur Deng ⋅ Nicholas Polizzi ⋅ Regina Barzilay ⋅ Tommi Jaakkola
Conformational sampling and interpolation using language-based protein folding neural networks
Diego del Alamo ⋅ Jeliazko Jeliazkov ⋅ Daphne Truan ⋅ Joel Karpiak
FLIGHTED: Inferring Fitness Landscapes from Noisy High-Throughput Experimental Data
Vikram Sundar ⋅ Boqiang Tu ⋅ Lindsey Guan ⋅ Kevin Esvelt
Contrasting Sequence with Structure: \\Pre-training Graph Representations with PLMs
Louis Robinson ⋅ Timothy Atkinson ⋅ Liviu Copoiu ⋅ Patrick Bordes ⋅ Thomas PIERROT ⋅ Thomas Barrett
Fast non-autoregressive inverse folding with discrete diffusion
John Yang ⋅ Jason Yim ⋅ Tommi Jaakkola ⋅ Regina Barzilay
Harmonic Prior Self-conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design
Hannes Stärk ⋅ Bowen Jing ⋅ Regina Barzilay ⋅ Tommi Jaakkola
CrysFormer: Protein Crystallography Prediction via 3d Patterson Maps and Partial Structure Attention
Chen Dun ⋅ Tom Pan ⋅ Shikai Jin ⋅ Ria Stevens ⋅ Mitchell D. Miller ⋅ George Phillips ⋅ Anastasios Kyrillidis
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris ⋅ Kieran Didi ⋅ Arian Jamasb ⋅ Chaitanya Joshi ⋅ Simon Mathis ⋅ Pietro Lió ⋅ Tom Blundell
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris ⋅ Kieran Didi ⋅ Arian Jamasb ⋅ Chaitanya Joshi ⋅ Simon Mathis ⋅ Pietro Lió ⋅ Tom Blundell
Sampling Protein Language Models for Functional Protein Design
Jeremie Theddy Darmawan ⋅ Yarin Gal ⋅ Pascal Notin
A framework for conditional diffusion modelling with applications in protein design
Kieran Didi ⋅ Francisco Vargas ⋅ Simon Mathis ⋅ Vincent Dutordoir ⋅ Emile Mathieu ⋅ Urszula Julia Komorowska ⋅ Pietro Lió
DiffRNAFold: Generating RNA Tertiary Structures with Latent Space Diffusion
Mihir Bafna ⋅ Vikranth Keerthipati ⋅ Subhash Kanaparthi ⋅ Ruochi Zhang
FlexiDock: Compositional diffusion models for flexible molecular docking
Zichen Wang ⋅ Balasubramaniam Srinivasan ⋅ Zhengyuan Shen ⋅ George Karypis ⋅ Huzefa Rangwala
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
Chuanrui WANG ⋅ Bozitao Zhong ⋅ Zuobai Zhang ⋅ Narendra Chaudhary ⋅ Sanchit Misra ⋅ Jian Tang
DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
Michael Plainer ⋅ Marcella Toth ⋅ Simon Dobers ⋅ Hannes Stärk ⋅ Gabriele Corso ⋅ Céline Marquet ⋅ Regina Barzilay
DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
Michael Plainer ⋅ Marcella Toth ⋅ Simon Dobers ⋅ Hannes Stärk ⋅ Gabriele Corso ⋅ Céline Marquet ⋅ Regina Barzilay
Transition Path Sampling with Boltzmann Generator-based MCMC Moves
Michael Plainer ⋅ Hannes Stärk ⋅ Charlotte Bunne ⋅ Stephan Günnemann
Inpainting Protein Sequence and Structure with ProtFill
Elizaveta Kozlova ⋅ Daniel Nakhaee-Zadeh Gutierrez ⋅ Arthur Valentin
Investigating Protein-DNA Binding Energetic of Mismatched DNA
Ruben Solozabal ⋅ Tamir Avioz ⋅ Yunxiang LI ⋅ Le Song ⋅ Martin Takac ⋅ Ariel Afek
AntiFold: Improved antibody structure design using inverse folding
Alissa M Hummer ⋅ Magnus H Høie ⋅ Tobias Olsen ⋅ Morten Nielsen ⋅ Charlotte Deane
Combining Structure and Sequence for Superior Fitness Prediction
Steffanie Paul ⋅ Pascal Notin ⋅ Aaron Kollasch ⋅ Debora Marks
Protein language models learn evolutionary statistics of interacting sequence motifs
Zhidian Zhang ⋅ Hannah Wayment-Steele ⋅ Garyk Brixi ⋅ Matteo Dal Peraro ⋅ Dorothee Kern ⋅ Sergey Ovchinnikov
FAFormer: Frame Averaging Transformer for Predicting Nucleic Acid-Protein Interactions
Tinglin Huang ⋅ Zhenqiao Song ⋅ Rex Ying ⋅ Wengong Jin
LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
Antoine Delaunay ⋅ Yunguan Fu ⋅ Nikolai Gorbushin ⋅ Robert McHardy ⋅ Bachir Djermani ⋅ Liviu Copoiu ⋅ Michael Rooney ⋅ Maren Lang ⋅ Andrey Tovchigrechko ⋅ Ugur Sahin ⋅ Karim Beguir ⋅ Nicolas Lopez Carranza
FrameDiPT: SE(3) Diffusion Model for Protein Structure Inpainting
Cheng ZHANG ⋅ Adam Leach ⋅ Thomas Makkink ⋅ Miguel Arbesú ⋅ Ibtissem Kadri ⋅ Daniel Luo ⋅ Liron Mizrahi ⋅ Sabrine Krichen ⋅ Maren Lang ⋅ Andrey Tovchigrechko ⋅ Nicolas Lopez Carranza ⋅ Ugur Sahin ⋅ Karim Beguir ⋅ Michael Rooney ⋅ Yunguan Fu
Validation of de novo designed water-soluble and membrane proteins by in silico folding and melting.
Alvaro Martin ⋅ Carolin Berner ⋅ Sergey Ovchinnikov ⋅ Anastassia Vorobieva
Validation of de novo designed water-soluble and membrane proteins by in silico folding and melting.
Alvaro Martin ⋅ Carolin Berner ⋅ Sergey Ovchinnikov ⋅ Anastassia Vorobieva
De Novo Short Linear Motif (SLiM) Discovery With AlphaFold-Multimer
Theo Sternlieb ⋅ ⋅ Davian Ho ⋅ Jeffrey Chan
AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2
Artem Gazizov ⋅ Anna Lian ⋅ Casper Goverde ⋅ Sergey Ovchinnikov ⋅ Nicholas Polizzi
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari ⋅ Nitya Thakkar ⋅ Rianne van den Berg ⋅ Alex X Lu ⋅ Nicolo Fusi ⋅ Ava Amini ⋅ Kevin Yang
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari ⋅ Nitya Thakkar ⋅ Rianne van den Berg ⋅ Alex X Lu ⋅ Nicolo Fusi ⋅ Ava Amini ⋅ Kevin Yang
Protein-Protein Docking with Latent Diffusion
Matt McPartlon ⋅ Céline Marquet ⋅ Tomas Geffner ⋅ Daniel Kovtun ⋅ Alexander Goncearenco ⋅ Zachary Carpenter ⋅ Luca Naef ⋅ Michael Bronstein ⋅ Jinbo Xu
SO(3)-Equivariant Representation Learning in 2D Images
Darnell Granberry ⋅ Alireza Nasiri ⋅ Jiayi Shou ⋅ Alex J. Noble ⋅ Tristan Bepler
HelixDiff: Conditional Full-atom Design of Peptides With Diffusion Models
Xuezhi Xie ⋅ Pedro A Valiente ⋅ Jisun Kim ⋅ Philip Kim
DIFFMASIF: Score-Based Diffusion Models for Protein Surfaces
Mehmet Akdel ⋅ Freyr Sverrisson ⋅ Dylan Abramson ⋅ Jean Feydy ⋅ Alexander Goncearenco ⋅ Yusuf Adeshina ⋅ Daniel Kovtun ⋅ Céline Marquet ⋅ Xuejin Zhang ⋅ David Baugher ⋅ Zachary Carpenter ⋅ Luca Naef ⋅ Michael Bronstein ⋅ Bruno Correia
FLAb: Benchmarking deep learning methods for antibody fitness prediction
Michael F Chungyoun ⋅ Jeffrey Ruffolo ⋅ Jeffrey Gray
Parameter-Efficient Fine Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions
Samuel Sledzieski ⋅ Meghana Kshirsagar ⋅ Rahul Dodhia ⋅ Bonnie Berger ⋅ Juan Lavista Ferres
Coarse-graining via reparametrization avoids force-matching and back-mapping
Nima Dehmamy ⋅ Csaba Both ⋅ Subhro Das ⋅ Tommi Jaakkola
SE3Lig: SE(3)-equivariant CNNs for the reconstruction of cofactors and ligands in protein structures
Guillaume Lamoureux ⋅ Sid Bhadra-Lobo ⋅ Anushriya Subedy ⋅ Sagar Khare
Cramming Protein Language Model Training in 24 GPU Hours
Nathan Frey ⋅ Taylor Joren ⋅ Aya Ismail ⋅ Allen Goodman ⋅ Stephen Ra ⋅ Kyunghyun Cho ⋅ Richard Bonneau ⋅ Vladimir Gligorijevic
Preparation Of Labeled Cryo-ET Datasets For Training And Evaluation Of Machine Learning Models
Aygul Ishemgulova ⋅ Alex J. Noble ⋅ Tristan Bepler ⋅ Alex De Marco
EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence
Aryan Tajmir Riahi ⋅ Chenwei Zhang ⋅ James Chen ⋅ Anne Condon ⋅ Khanh Dao Duc
Fast protein backbone generation with SE(3) flow matching
Jason Yim ⋅ Andrew Campbell ⋅ Yue Kwang Foong ⋅ Sarah Lewis ⋅ Victor Satorras ⋅ Michael Gastegger ⋅ Bas Veeling ⋅ Jose Jimenez-Luna ⋅ Regina Barzilay ⋅ Tommi Jaakkola ⋅ Frank Noe
Frame2seq: structure-conditioned masked language modeling for protein sequence design
Deniz Akpinaroglu ⋅ Kosuke Seki ⋅ Eleanor Zhu ⋅ Tanja Kortemme
Structure-Conditioned Generative Models for De Novo Ligand Generation: A Pharmacophore Assessment
Shannon Smith ⋅ Leo Gendelev ⋅ Kangway Chuang ⋅ Seth Harris
Jointly Embedding Protein Structures and Sequences through Residue Level Alignment
Foster Birnbaum ⋅ Saachi Jain ⋅ Amy Keating ⋅ Aleksander Madry
Evaluating Representation Learning on the Protein Structure Universe
Arian Jamasb ⋅ Alex Morehead ⋅ Zuobai Zhang ⋅ Chaitanya K. Joshi ⋅ Kieran Didi ⋅ Simon Mathis ⋅ Charles Harris ⋅ Jian Tang ⋅ Jianlin Cheng ⋅ Pietro Lió ⋅ Tom Blundell
Enhancing Antibody Language Models with Structural Information
Justin Barton ⋅ Jacob Galson ⋅ Jinwoo Leem
Amortized Pose Estimation for X-Ray Single Particle Imaging
Jay Shenoy ⋅ Axel Levy ⋅ Frederic Poitevin ⋅ Gordon Wetzstein
Rethinking Performance Measures of RNA Secondary Structure Problems
Frederic Runge ⋅ Jörg Franke ⋅ Daniel Fertmann ⋅ Frank Hutter
Structure-based and leakage-free data splits for rigorous protein function evaluation
Charlotte Rochereau ⋅ Mohammed AlQuraishi ⋅ Arthur Valentin ⋅ Gergo Nikolenyi
Uncovering sequence diversity from a known protein structure
Luca Alessandro Silva ⋅ Barthélémy Meynard ⋅ Carlo Lucibello ⋅ Christoph Feinauer
Exploiting language models for protein discovery with latent walk-jump sampling
Sai Pooja Mahajan ⋅ Nathan Frey ⋅ Dan Berenberg ⋅ Joseph Kleinhenz ⋅ Richard Bonneau ⋅ Vladimir Gligorijevic ⋅ Andrew Watkins ⋅ Saeed Saremi