Workshop
Integrating Generative and Experimental Platforms for Biomolecular Design
Chenghao Liu · Jarrid Rector-Brooks · Soojung Yang · Sidney Lisanza · Francesca-Zhoufan Li · Hannes Stärk · Jacob Gershon · Lauren Hong · Pranam Chatterjee · Tommi Jaakkola · Regina Barzilay · David Baker · Frances Arnold · Yoshua Bengio
Hall 4 #4
Sat 26 Apr, 5:50 p.m. PDT
Biomolecular design, through artificial engineering of proteins, ligands, and nucleic acids, holds immense promise in addressing pressing medical, industrial, and environmental challenges. While generative machine learning has shown significant potential in this area, a palpable disconnect exists with experimental biology: many ML research efforts prioritize static benchmark performance, potentially sidelining impactful biological applications. This workshop seeks to bridge this gap by bringing computationalists and experimentalists together, catalyzing a deeper interdisciplinary discourse. Together, we will explore the strengths and challenges of generative ML in biology, experimental integration of generative ML, and biological problems ready for ML. To attract high-quality and diverse research, we partnered with Nature Biotechnology for a special collection, and we created dedicated tracks for in-silico ML research and hybrid ML-experimental biology research. Our lineup features emerging leaders as speakers and renowned scientists as panelists, encapsulating a spectrum from high-throughput experimentation and computational biology to generative ML. With a diverse organizing team and backed by industry sponsors, we dedicate the workshop to pushing the boundaries of ML's role in biology.
Schedule
Sat 5:50 p.m. - 6:00 p.m.
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Opening Remarks
SlidesLive Video |
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Sat 6:00 p.m. - 6:30 p.m.
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Kotaro Tsuboyama
SlidesLive Video |
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Sat 6:30 p.m. - 7:00 p.m.
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Florian Hollfelder
SlidesLive Video |
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Sat 7:00 p.m. - 7:15 p.m.
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Coffee break 1
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Sat 7:15 p.m. - 7:30 p.m.
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Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding
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Oral
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SlidesLive Video |
Yasha Ektefaie · Olivia Viessmann · Siddharth Narayanan · Drew Dresser · J. Kim · Armen Mkrtchyan 🔗 |
Sat 7:30 p.m. - 7:45 p.m.
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Programmable Protein Stabilization with Language Model-Derived Peptide Guides
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Oral
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SlidesLive Video |
12 presentersLauren Hong · Tian Wang · Divya Srijay · Howard Liu · Rio Watson · Lin Zhao · Sophia Vincoff · Tianlai Chen · Kseniia Kholina · Shrey Goel · Matthew DeLisa · Pranam Chatterjee |
Sat 7:45 p.m. - 8:00 p.m.
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EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
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Oral
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SlidesLive Video |
Allan Costa · Ilan Mitnikov · Franco Pellegrini · Ameya Daigavane · Mario Geiger · Zhonglin Cao · Karsten Kreis · Tess Smidt · Emine Kucukbenli · JOSEPH JACOBSON 🔗 |
Sat 8:00 p.m. - 8:05 p.m.
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Preventing cell-to-cell tranmission of disordered proto-fibrils of $\alpha$-Synuclein
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Lightning
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link
SlidesLive Video |
Akshay Chenna 🔗 |
Sat 8:05 p.m. - 8:10 p.m.
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Inverse problems with experiment-guided AlphaFold
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Lightning
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SlidesLive Video |
Sai Advaith Maddipatla · Nadav Bojan · Meital Bojan · Sanketh Vedula · Ailie Marx · Paul Schanda · Alexander Bronstein 🔗 |
Sat 8:10 p.m. - 8:15 p.m.
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Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
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Lightning
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SlidesLive Video |
Tony Shen · Seonghwan Seo · Ross Irwin · Kieran Didi · Simon Olsson · Woo Youn Kim · Martin Ester 🔗 |
Sat 8:15 p.m. - 9:15 p.m.
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Poster session 1
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Sat 9:15 p.m. - 10:00 p.m.
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Lunch break (catering provided)
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Sat 10:00 p.m. - 10:30 p.m.
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Charlotte Bunne
SlidesLive Video |
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Sat 10:30 p.m. - 10:45 p.m.
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Fast and Accurate Antibody Sequence Design via Structure Retrieval
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Oral
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SlidesLive Video |
Xingyi Zhang · Kun XIE · Ningqiao Huang · Wei Liu · Peilin Zhao · Sibo WANG · Kangfei Zhao · Biaobin Jiang 🔗 |
Sat 10:45 p.m. - 11:00 p.m.
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Multiplexed DNA Assembly from Oligo-pools
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Oral
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SlidesLive Video |
Shaozhong Zou · zhien wu · Chunfu Xu 🔗 |
Sat 11:00 p.m. - 11:15 p.m.
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Decoding the Mechanistic Impact of Genetic Variation on Regulatory Sequences with Deep Learning
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Oral
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link
SlidesLive Video |
Evan Seitz · Peter Koo · Justin Kinney · David McCandlish 🔗 |
Sat 11:15 p.m. - 11:20 p.m.
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A generalized protein design foundation model enables generation of functional de novo proteins
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Lightning
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SlidesLive Video |
Timothy Riley · Oleg Matusovsky · Mohammad Parsa · Pourya Kalantari · Kooshiar Azimian · Kathy Wei 🔗 |
Sat 11:20 p.m. - 11:25 p.m.
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SOAPI: Siamese-guided generation of Off-Target-Avoiding Protein Interactions
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Lightning
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SlidesLive Video |
Sophia Vincoff · Oscar Davis · Alexander Tong · Joey Bose · Pranam Chatterjee 🔗 |
Sat 11:25 p.m. - 11:35 p.m.
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Coffee break 2
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Sat 11:35 p.m. - 12:05 a.m.
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Michael Schaarschmidt
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Sun 12:05 a.m. - 1:05 a.m.
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Panel discussion
SlidesLive Video |
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Sun 1:05 a.m. - 1:20 a.m.
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Sponsor presentations
SlidesLive Video |
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Sun 1:20 a.m. - 2:20 a.m.
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Poster session 2 & seed grant pitching
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Sun 2:20 a.m. - 2:30 a.m.
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Closing remarks & awards
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Guided Sequence-Structure Generative Modeling for Iterative Antibody Optimization ( Poster ) > link | Aniruddh Raghu · Sebastian W. Ober · Maxwell Kazman · Hunter Elliott 🔗 |
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Interpreting and Steering Protein Language Models through Sparse Autoencoders ( Poster ) > link | Edith Natalia Villegas Garcia · Alessio ansuini 🔗 |
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Residue-level text conditioning for protein language model mutation effect prediction ( Poster ) > link |
11 presentersDan Berenberg · Nate Gruver · Alan Amin · Peter Mørch Groth · Tianlai Chen · Harsh Srivastava · Pascal Notin · Debora Marks · Andrew Gordon Wilson · Kyunghyun Cho · Richard Bonneau |
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RNAGym: Benchmarks for RNA Fitness and Structure Prediction ( Poster ) > link |
12 presentersRohit Arora · Murphy Angelo · Christian Choe · Aaron Kollasch · Fiona Qu · Courtney Shearer · Ruben Weitzman · Artem Gazizov · Sarah Gurev · Erik Xie · Debora Marks · Pascal Notin |
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Preferential Multi-Objective Bayesian Optimization for Drug Discovery ( Poster ) > link | Tai Dang · Long-Hung Pham · Sang Truong · Ari Glenn · Wendy Nguyen · Edward Pham · Jeffrey Glenn · Sanmi Koyejo · Thang Luong 🔗 |
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Steering Generative Models with Experimental Data for Protein Fitness Optimization ( Poster ) > link | Jason Yang · Wenda Chu · Daniel Khalil · Raul Astudillo · Bruce Wittmann · Frances Arnold · Yisong Yue 🔗 |
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Flow-Based Fragment Identification via Contrastive Learning of Binding Site-Specific Latent Representations ( Poster ) > link | Rebecca M Neeser · Ilia Igashov · Arne Schneuing · Michael Bronstein · Philippe Schwaller · Bruno Correia 🔗 |
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Programming co-folding to design binders for intrinsically disordered epitopes ( Poster ) > link | Jakub Lála · Daniele Visco · Stefano Angioletti-Uberti 🔗 |
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Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule ( Poster ) > link | Keyue Qiu · Yuxuan Song · Zhehuan Fan · Peidong Liu · Zhe Zhang · Mingyue Zheng · Hao Zhou · Wei-Ying Ma 🔗 |
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Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional ( Poster ) > link | Sanjeev Raja · Martin Sipka · Michael Psenka · Tobias Kreiman · Michal Pavelka · Aditi Krishnapriyan 🔗 |
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Gumbel-Softmax Score and Flow Matching for Discrete Biological Sequence Generation ( Poster ) > link | Sophia Tang · Yinuo Zhang · Alexander Tong · Pranam Chatterjee 🔗 |
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Sampling Protein Language Models for Functional Protein Design ( Poster ) > link | Jeremie Theddy Darmawan · Yarin Gal · Pascal Notin 🔗 |
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Test-Time View Selection for Multi-Modal Decision Making ( Poster ) > link | Eeshaan Jain · Johann Wenckstern · Benedikt von Querfurth · Charlotte Bunne 🔗 |
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From Minimal Data To Maximal Insight: A Machine Learning Guided Platform For Peptide Discovery ( Poster ) > link |
14 presentersPouriya Bayat · Spencer Perkins · Sebastian Clancy · Sahil Patel · Richard Yin · Krištof Bozovičar · Idorenyin IWE · Mohammad Simchi · Ilan Zeisler · Serena Singh · Vivian White · Matthew Xie · Sean Palter · Keith Pardee |
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Antibody design using preference optimization and structural inference ( Poster ) > link | Archit Vasan · Gautham Dharuman · Ozan Gokdemir · Heng Ma · Arvind Ramanathan 🔗 |
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Guided Generation of B-cell Receptors with Conditional Walk-Jump Sampling ( Poster ) > link |
14 presentersTaylor Joren · Sarah Robinson · Homa MohammadiPeyhani · Sai Pooja Mahajan · Edith Lee · Stephen Lillington · Qixin Bei · Saeed Saremi · Jae Hyeon Lee · Richard Bonneau · Isidro Hotzel · Vladimir Gligorijevic · Simon Kelow · Nathan Frey |
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Implicit Bayesian Markov Decision Process for Resource-Efficient Experimental Design in Drug Discovery ( Poster ) > link | Tianchi Chen · Jan Bíma · Sean Wu · Otto Ritter · Bo Yuan · Bingjia Yang · Xiang Yu 🔗 |
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Towards Protein Sequence & Structure Co-Design with Multi-Modal Language Models ( Poster ) > link | Stephen Lu · Jiarui Lu · Hongyu Guo · Jian Tang 🔗 |
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A Guided Design Framework for the Optimization of Therapeutic-like Antibodies ( Poster ) > link |
14 presentersAmy Wang · Zhe Sang · Samuel Stanton · Jennifer L Hofmann · Saeed Izadi · Eliott Park · Jan Ludwiczak · Matthieu Kirchmeyer · Darcy Davidson · Andrew Maier · Tom Pritsky · Nathan Frey · Franziska Seeger · Andrew Watkins |
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SYNEVO: towards synthetic evolution of biomolecules via aligning protein language models to biological hardware ( Poster ) > link | Maria Artigues-Lleixà · Eduard Sune Morote · Filippo Stocco · Noelia Ferruz · Marc Güell 🔗 |
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AI-guided data-scarce engineering of RfxCas13d to create a cell selection tool ( Poster ) > link | Han Spinner · Ayush Noori · Debora Marks · George Church · Lisa Riedmayr 🔗 |
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Towards Scaling Laws for Language Model Powered Evolutionary Algorithms: Case Study on Molecular Optimization ( Poster ) > link | Tigran Fahradyan · Filya Geikyan · Philipp Guevorguian · Hrant Khachatrian 🔗 |
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CAMP: COMBINATORIAL ENGINEERING OF PROTEINS ( Poster ) > link | MANVITHA PONNAPATI · Brian Lynch · Sapna Sinha · Edward Boyden · JOSEPH JACOBSON 🔗 |
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A data guided approach to building an ML ready protein expression dataset ( Poster ) > link | Catherine Baranowski · Han Spinner · Peter Kelly 🔗 |
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OPUS-GO: Unlocking Residue-level Insights from Sequence-level Annotations Using Biological Language Models ( Poster ) > link | Gang Xu · Ying Lv · Ruoxi Zhang · Xinyuan Xia · Qinghua Wang · Jianpeng Ma 🔗 |
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MeMDLM: De Novo Membrane Protein Design with Property-Guided Discrete Diffusion ( Poster ) > link | Shrey Goel · Vishrut Thoutam · Edgar M. Marroquin · Aaron Gokaslan · Arash Firouzbakht · Sophia Vincoff · Volodymyr Kuleshov · Huong Kratochvil · Pranam Chatterjee 🔗 |
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Few-shot active learning for de novo dual-target peptide design with high bio-activity ( Poster ) > link | Tianxu Lv · Bing He · Yuran Jia · Xiang pan · Jianhua Yao 🔗 |
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Scaling Deep Learning Solutions for Transition Path Sampling ( Poster ) > link | Jungyoon Lee · Michael Plainer · Yuanqi Du · Lars Holdijk · Rob Brekelmans · Carla Gomes · Dominique Beaini · Kirill Neklyudov 🔗 |
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Large Drug Discovery Model ( Poster ) > link | Ilia Igashov · Arne Schneuing · Adrian Dobbelstein · Irina Morozova · Rebecca M Neeser · Evgenia Elizarova · Philippe Schwaller · Michael Bronstein · Bruno Correia 🔗 |
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Scaling Sparse Autoencoders to Interpret Protein Structure Prediction ( Poster ) > link | John J. Yang · David Yang · Nithin Parsan 🔗 |
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TCR-TRANSLATE: CONDITIONAL GENERATION OF REAL ANTIGEN- SPECIFIC T-CELL RECEPTOR SEQUENCES ( Poster ) > link | Dhuvarakesh Karthikeyan · Colin Raffel · Benjamin Vincent · Alex Rubinsteyn 🔗 |
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Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques ( Poster ) > link | Eva Smorodina · Victor Greiff · Puneet Rawat · Rahmad Akbar · Oliver Crook · Khang Quý · Brij Mehta · Fridtjof Lund-Johansen 🔗 |
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PickPocket Enables Binding Site Prediction at the Proteome Scale ( Poster ) > link | Stelina Tarasi · Laura Malo · Alexis Molina 🔗 |
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ACTIVE LEARNING ON SYNTHONS FOR MOLECULAR DESIGN ( Poster ) > link | Tom Grigg · Mason Burlage · Oliver Scott · Dominique Sydow · Liam Wilbraham 🔗 |
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PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion ( Poster ) > link | Sophia Tang · Yinuo Zhang · Pranam Chatterjee 🔗 |
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Conformation-specific Design: a New Benchmark and Algorithm with Application to Engineer a Constitutively Active MAP Kinase ( Poster ) > link | Jacob Stern · Siba Alharbi · Anandsukeerthi Sandholu · Stefan Arold · Dennis Della Corte 🔗 |
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An evaluation of unconditional 3D molecular generation methods ( Poster ) > link | Martin Buttenschoen · Yael Ziv · Garrett Morris · Charlotte Deane 🔗 |
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A Data-Driven Approach to Antigen-Antibody Complex Structure Modeling Using Labeled VHH Antibodies ( Poster ) > link | Takashi Nagata · Hiroyuki Yamazaki · Ryota Maeda · Hirofumi Tsuruta · Ryotaro Tamura · Akihiro Imura 🔗 |
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ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation's Functional Effect ( Poster ) > link | Moritz Glaser 🔗 |
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A latent back-projection network for novel projection synthesis for improved Cryo-ET ( Poster ) > link | Robert Kiewisz · Gabriel Meyer-Lee · Tristan Bepler 🔗 |
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Structure-based synthetic data augmentation for protein language models ( Poster ) > link | Alex Lee · Ava Amini · Kevin K Yang · Sarah Alamdari · Chentong Wang · Reza Abbasi-Asl 🔗 |
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Molecular Property Prediction using Pretrained-BERT and Bayesian Active Learning: A Data-Efficient Approach to Drug Design ( Poster ) > link | Muhammad Arslan Masood · Samuel Kaski · Tianyu Cui 🔗 |
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Structure-Aware Language Models Trained on Ultra-Mega-Scale Metagenomic Data Improve Protein Folding Stability Prediction ( Poster ) > link | Yehlin Cho · Kotaro Tsuboyama · Gabriel Rocklin · Sergey Ovchinnikov 🔗 |
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Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning ( Poster ) > link | Manel Gil-Sorribes · Alvaro Ciudad Serrano · Alexis Molina 🔗 |
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GROQ-seq: A Collaborative, Open Data Approach to Addressing Protein Function Prediction ( Poster ) > link |
11 presentersDavid Ross · Han Spinner · Simon dOelsnitz · Svetlana Ikonomova · Olga Vasilyeva · Nina Alperovich · Kristen Sheldon · Courtney Tretheway · Dana Cortade · Erika DeBenedictis · Peter Kelly |
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moPPIt: De Novo Generation of Motif-Specific Peptide Binders via Conditional Uniform Discrete Diffusion ( Poster ) > link | Tong Chen · Yinuo Zhang · Pranam Chatterjee 🔗 |
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Addressing Model Overcomplexity in Drug-Drug Interaction Prediction With Molecular Fingerprints ( Poster ) > link | Manel Gil-Sorribes · Alexis Molina 🔗 |
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Learning Representations of Instruments for Partial Identification of Treatment Effects ( Poster ) > link | Jonas Schweisthal · Dennis Frauen · Maresa Schröder · Konstantin Hess · Niki Kilbertus · Stefan Feuerriegel 🔗 |
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Mol-MoE: Training Preference-Guided Routers for Molecule Generation ( Poster ) > link | Diego Calanzone · Pierluca D'Oro · Pierre-Luc Bacon 🔗 |
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RNA-EFM : Energy based Flow Matching for Protein-conditioned RNA Sequence-Structure Co-design ( Poster ) > link | Abrar Abir · Liqing Zhang 🔗 |
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Reframing Retreival-Augmented Generation for *in silico* optimization of antibody solubility ( Poster ) > link | Lena Erlach · Rohit Singh · Bonnie Berger · Sai Reddy 🔗 |
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FLOWR -- Flow Matching for Structure- and Interaction-Aware De Novo Ligand Generation ( Poster ) > link | Julian Cremer · Ross Irwin · Alessandro Tibo · Jon Paul Janet · Simon Olsson · Djork-Arné Clevert 🔗 |
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Assessing Quantization and Efficient Fine-Tuning for Protein Language Models ( Poster ) > link | Sebastian Clancy · Ilan Zeisler · Pouriya Bayat · Matthew Xie · Vivian White · Spencer Perkins · Sepehr Bayat · Keith Pardee 🔗 |
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Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design ( Poster ) > link | Nianzu Yang · jian ma · Songlin Jiang · Huaijin Wu · Shuangjia Zheng · Wengong Jin · Junchi Yan 🔗 |
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Engineering modular bacteriophage genomes for targeted bacterial elimination ( Poster ) > link | Sriharshita Musunuri 🔗 |
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Substrate-aware Zero-Shot Predictors for Non-Native Enzyme Activities
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Lightning
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Francesca-Zhoufan Li · LUKAS ALEXANDER RADTKE · Kadina Johnston · Chenghao Liu · Yisong Yue · Frances Arnold 🔗 |
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Molecular design using graph Bayesian optimization with shortest-path kernels ( Poster ) > link | Yilin Xie · Shiqiang Zhang · Jixiang Qing · Ruth Misener · Calvin Tsay 🔗 |
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Higher-Order Molecular Learning: The Cellular Transformer ( Poster ) > link |
11 presentersMelih Barsbey · Rubén Ballester · Andac Demir · Carles Casacuberta · Pablo Hernández-García · David Pujol-Perich · Sarper Yurtseven · Sergio Escalera · Claudio Battiloro · Mustafa Hajij · Tolga Birdal |
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AffinityFlow: Guided Flows for Antibody Affinity Maturation ( Poster ) > link | Can Chen · Karla-Luise Herpoldt · Chenchao Zhao · Zichen Wang · Marcus Collins · Shang Shang · Ron Benson 🔗 |
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Gradient GA: Gradient Genetic Algorithm for Drug Molecular Design ( Poster ) > link | Chris Zhuang · Debadyuti Mukherjee · Yingzhou Lu · Tianfan Fu · Ruqi Zhang 🔗 |
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GENERATIVE PROTEIN DESIGN FOR OVERLAPPING GENES ( Poster ) > link | Chenling Xu · Jennifer Chlebek · Jonathan Allen · Hunter Nisonoff · Dan Park 🔗 |
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IgCraft: A versatile sequence generation framework for antibody discovery and engineering ( Poster ) > link | Matthew Greenig · Haowen Zhao · Vladimir Radenkovic · Aubin Ramon · Pietro Sormanni 🔗 |
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Bio2Token: All-atom tokenization of any biomolecular structure with Mamba ( Poster ) > link | Andrew Liu · Axel Elaldi · Nathan Russell · Olivia Viessmann 🔗 |
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Hierarchical Protein Backbone Generation with Latent and Structure Diffusion ( Poster ) > link | Jason Yim · Marouane Jaakik · Ge Liu · Jacob Gershon · Karsten Kreis · David Baker · Regina Barzilay · Tommi Jaakkola 🔗 |
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Sequence-based protein models for the prediction of mutations across priority viruses ( Poster ) > link | Sarah Gurev · Noor Youssef · Navami Jain · Debora Marks 🔗 |
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Exploring zero-shot structure-based protein fitness prediction ( Poster ) > link | Arnav Sharma · Anthony Gitter 🔗 |
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Design of Ligand-Binding Proteins with Atomic Flow Matching ( Poster ) > link | Junqi Liu · Shaoning Li · Chence Shi · Zhi Yang · Jian Tang 🔗 |
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EVOLUTIONARY POLICY GRADIENT BASED OPTIMIZATION FOR SMALL MOLECULE DRUG DISCOVERY ( Poster ) > link | Tehemton Khairabadi · Vishal Pagidipally 🔗 |
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Metalorian: De Novo Generation of Heavy Metal-Binding Peptides with Classifier-Guided Diffusion Sampling ( Poster ) > link | Yinuo Zhang · Divya Srijay · Pranam Chatterjee 🔗 |
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Protein structure predictors implicitly define binding energy functions ( Poster ) > link | Divya Nori · Caroline Uhler · Wengong Jin 🔗 |
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SweetBERT: exploring BERT-based models for IUPAC glycan nomenclature modeling ( Poster ) > link | Irene Rubia-Rodríguez · Henrik Nielsen · Garry Gippert · Kristian Barrett · Bernard Henrissat · Ole Winther 🔗 |
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Targeting Aggregating Proteins with Language Model-Designed Degraders ( Poster ) > link | Rio Watson · Kishan Patel · Pranam Chatterjee 🔗 |
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De Novo Design of Antigen-Specific Antibodies Using Structural Constraint-Based Generative Language Model ( Poster ) > link | Yuran Jia · Bing He · Tianxu Lv · YangXiao · Tianyi Zhao · Jianhua Yao 🔗 |
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It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design ( Poster ) > link | Jeff Guo · Philippe Schwaller 🔗 |
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Scalable and Cost-Efficient de Novo Template-Based Molecular Generation ( Poster ) > link | Piotr Gaiński · Oussama Boussif · Dmytro Shevchuk · Andrei Rekesh · Ali Parviz · Mike Tyers · Robert Batey · Michał Koziarski 🔗 |
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Why risk matters for protein binder design ( Poster ) > link | Tudor-Stefan Cotet · Igor Krawczuk 🔗 |
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All-Atom Protein Generation with Latent Diffusion ( Poster ) > link | Amy Lu · Wilson Yan · Sarah Robinson · Simon Kelow · Kevin K Yang · Vladimir Gligorijevic · Kyunghyun Cho · Richard Bonneau · Pieter Abbeel · Nathan Frey 🔗 |
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Sesame: Opening the door to protein pockets ( Poster ) > link | Raúl Miñán · Carles Perez-Lopez · Javier Iglesias-Fernández · Alvaro Ciudad Serrano · Alexis Molina 🔗 |
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FragFM: Efficient Fragment-Based Molecular Generation via Discrete Flow Matching ( Poster ) > link | Joongwon Lee · Seonghwan Kim · Woo Youn Kim 🔗 |
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GLID$^2$E: A Gradient-Free Lightweight Fine-tune Approach for Discrete Sequence Design ( Poster ) > link | Hanqun Cao · Haosen Shi · Chenyu Wang · Sinno Jialin Pan · Pheng-Ann Heng 🔗 |
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Towards More Accurate Full-Atom Antibody Co-Design ( Poster ) > link | Jiayang Wu · Xingyi Zhang · Xiangyu Dong · Kun XIE · Ziqi Liu · Wensheng Gan · Sibo WANG · Le Song 🔗 |
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Efficient Molecular Conformer Generation with SO(3) Averaged Flow-Matching and Reflow ( Poster ) > link | Zhonglin Cao · Mario Geiger · Allan Costa · Danny Reidenbach · Karsten Kreis · Tomas Geffner · Franco Pellegrini · Guoqing Zhou · Emine Kucukbenli 🔗 |
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A Mammalian High-Throughput Assay to Screen AI-Designed Protein Degraders ( Poster ) > link | Lin Zhao · Aastha Pal · Tong Chen · Pranam Chatterjee 🔗 |
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Aligning Chemical and Protein Language Models with Continuous Feedback using Energy Rank Alignment ( Poster ) > link | Shriram Chennakesavalu · Frank Hu · Sebastian Ibarraran · Grant Rotskoff 🔗 |
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AlphaSAXS: Reconstructing Protein Structure with Physiologically Relevant Conformations from X-ray Scattering Data ( Poster ) > link | Feng Yu · Stephanie Prince · Andrew Tritt · Kanupriya Pande · Greg Hura · Oliver Ruebel · Susan Tsutakawa 🔗 |