Accepted Papers

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Poster
San Diego
Exploring simulators for particle picking in cryo-electron tomography

Serena Arghittu et al.

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Poster
Copenhagen
Leveraging in Silico Predictors for Antibody Design via Multi-Objective Bayesian Optimization

Jackie Rao et al.

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Poster
Copenhagen
Self Distillation Fine-Tuning of Protein Language Models Improves Versatility in Protein Design

Amin Tavakoli et al.

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Poster
San Diego
REPTRA: Mapping Immune T Cell Receptor Activity from Full Sequences with a Debiased Contrastive Loss

John Abel et al.

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Poster
San Diego
Reciprocal Best Matching: a new pipeline for scoring models with unknown stoichiometry in CASP experiments

Rongqing Yuan et al.

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Contributed talk
Copenhagen
AbTune: layer-wise selective Fine-Tuning of protein language models for Antibodies

Xiaotong Xu

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Poster
San Diego
Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching

Da Xu et al.

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Poster
San Diego
Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning

Jiayi Xin et al.

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Poster
San Diego
ChromWeave: Equivariant Generative Modeling of 3D Genome Organization

Shuming Liu et al.

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Poster
San Diego
SimpleFold: Folding Proteins is Simpler than You Think

Yuyang Wang et al.

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Poster
San Diego
Learning residue level protein dynamics with multiscale Gaussians

Mihir Bafna et al.

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Poster
San Diego
Generating functional and multistate proteins with a multimodal diffusion transformer

Bowen Jing et al.

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Poster
San Diego
TLDR: RL-guided latent diffusion for de novo TCR design

Soo Kim et al.

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Poster
Copenhagen
g-DPO: Scalable Preference Optimization for Protein Language Models

Constance Ferragu et al.

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Poster
Copenhagen
A deep learning approach for rational affinity maturation of anti-VEGF nanobodies

Gaëlle Verdon et al.

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Poster
San Diego
PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding

Giosue Migliorini et al.

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Poster
San Diego
Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding

Elliot Layne et al.

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Poster
San Diego
Conditional Protein Structure Generation with Protpardelle-1c

Tianyu Lu et al.

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Poster
San Diego
MSACLR: Contrastive Learning of Protein Conformations from MSAs

JUNJIE ZHANG et al.

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Contributed talk
San Diego
Ensemble-conditioned protein sequence design with Caliby

Richard Shuai et al.

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Poster
Copenhagen
Multi-Scale Protein Structure Modelling with Geometric Graph U-Nets

Chang Liu et al.

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Contributed talk
Copenhagen
Computational Design of Monomeric Variants of Multimeric Enzymes

Jakub Lála et al.

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Poster
Copenhagen
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design

Zygimantas Jocys et al.

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Poster
Copenhagen
Stoic: Fast and accurate protein stoichiometry prediction

Daniil Litvinov et al.

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Poster
San Diego
De novo generation of functional terpene synthases using TpsGPT

Hamsini Ramanathan et al.

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Contributed talk
Copenhagen
ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions

Cyril Malbranke et al.

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Poster
Copenhagen
PrOMet: Accurate and Robust Metal-binding site and Type Prediction

Gangeun Park et al.

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Contributed talk
Copenhagen
Rewriting protein alphabets with language models

Lorenzo Pantolini et al.

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Poster
San Diego
Design of peptides with non-canonical amino acids using flow matching

Jin Sub Lee et al.

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Poster
San Diego
FALCON: Few-step Accurate Likelihoods for Continuous Flows

Danyal Rehman et al.

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Poster
Copenhagen
Improving RNA 3D Structure Prediction via Language Model-Augmented AlphaFold 3

Shuxian Zou et al.

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Poster
San Diego
Look mom, no experimental data! Learning to score protein-ligand interactions from simulations

Michael Brocidiacono et al.

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Poster
San Diego
forge: sequence-based binder design with latent flow matching

Young Su Ko

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Poster
San Diego
FlashAffinity: Bridging the Accuracy-Speed Gap in Protein-Ligand Binding Affinity Prediction

Songlin Jiang et al.

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Poster
Copenhagen
Synthetic Evolution of Enzyme Specificity with a Self-Driving Laboratory

Coban Brooks et al.

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Poster
San Diego
Do biological autoregressive models learn protein coevolution?

Xiaonan Liu

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Contributed talk
San Diego
SwitchCraft: Programmatic Design of State-Switching Proteins

Bowen Jing et al.

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Poster
San Diego
Backprop-based Motif Scaffolding Beats Generative Models

Anisha Parsan et al.

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Poster
San Diego
Conformational Rank Conditioned Committees for Machine Learning-Assisted Directed Evolution

Mia Adler et al.

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Poster
San Diego
Inferring Local Protein Structural Similarity from Sequence Alone

Zinnia Ma et al.

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Poster
San Diego
DiffAlign: Diffusion-Based Molecular Alignment with Pocket-Aware Guidance

Iljung Kim et al.

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Poster
San Diego
BioBlobs: Differentiable Graph Partitioning for Protein Representation Learning

Xin Wang et al.

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Poster
San Diego
OMTRA: A Multi-Task Generative Model for Structure-Based Drug Design

Ian Dunn et al.

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Poster
San Diego
Improving scoring functions for protein-protein docking with LambdaLoss

Richard Zhu et al.

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Poster
Copenhagen
Real-time Forecasting of Influenza Evolution

Aarushi Mehrotra et al.

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Poster
San Diego
All-atom protein design via SE(3) flow matching with ProteinZen

Alex Li et al.

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Contributed talk
San Diego
Can Biomolecular Structure Predictors Generalize to Alternative Conformations?

Karson Chrispens et al.

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Poster
San Diego
Biophysical Priors Enhance Protein-Protein Binding DDG Prediction

Antoine Maechler et al.

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Contributed talk
San Diego
TaxoFormer: Hierarchical Transformer for Predicting the Full Taxonomic Lineage of Protein Sequences

Mohammad Parsa et al.

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Poster
Copenhagen
Structure-Aware Mapping of Disease-Relevant Missense Variation: A Case Study in Three Nuclear Pore Complex Genes

Fatemeh Yekeh Yazdandoost et al.

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Poster
San Diego
FlexVASP-S: Flexible Steric-Aware 3D Geometric Framework for Explaining Protein Binding Specificity

Yangying Liu et al.

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Poster
San Diego
Improving nanobody structure prediction with self-distillation

Montader Ali et al.

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Poster
San Diego
TangledFeatures: Robust Feature Selection in Highly Correlated Spaces

Allen Sunny

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Poster
Copenhagen
GlycoGym: Benchmarking Glycan Property Prediction

Roman Joeres et al.

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Poster
San Diego
Curriculum-Augmented GFlowNets For mRNA Sequence Generation

Aya Laajil et al.

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Contributed talk
Copenhagen
ProFam: an open protein family language model for functional protein design

Jude Wells et al.

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Poster
Copenhagen
MomeDTA: Improving Generalizability in Drug-Target Affinity Prediction by Mixture of Multi-view Experts

Qingyu Yang et al.

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Poster
Copenhagen
Seek and You Shall Fold

Nadav Bojan Sellam et al.

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Poster
Copenhagen
On fine-tuning Boltz-2 for protein-protein affinity prediction

James King et al.

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Poster
San Diego
Mechanistic Interpretability of Antibody Language Models Using SAEs

Rebonto Haque et al.

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Sponsors US Edition

Xaira
Generate
Biohub
Latent Labs
Terray Therapeutics
Rosetta Commons
Atomic AI
Flex Therapeutics
Third Rock

Sponsors EU Edition

Cradle
Adaptyv

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