23 citations · 54 across the 14 of their papers we have counts for
14 papers
Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute
Kieran Didi, Zuobai Zhang, Guoqing Zhou +11
Protein interaction modeling is central to protein design, which has been transformed by machine learning with applications in drug discovery and beyond. In this landscape, structu…
Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
Danny Reidenbach, Zhonglin Cao, Zuobai Zhang +8
High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pair…
Flows, straight but not so fast: Exploring the design space of Rectified Flows in Protein Design
Junhua Chen, Simon Mathis, Charles Harris +2
Generative modeling techniques such as Diffusion and Flow Matching have achieved significant successes in generating designable and diverse protein backbones. However, many current…
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
Tomas Geffner, Kieran Didi, Zhonglin Cao +6
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointl…
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
Tony Shen, Seonghwan Seo, Ross Irwin +4
Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Gen…
Proteina: Scaling Flow-based Protein Structure Generative Models
Tomas Geffner, Kieran Didi, Zuobai Zhang +8
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale…
MotifBench: A standardized protein design benchmark for motif-scaffolding problems
Zhuoqi Zheng, Bo Zhang, Kieran Didi +5
The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a mot…
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery
Peter St. John, Dejun Lin, Polina Binder +89
Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increas…
Evaluating representation learning on the protein structure universe
Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi +8
We introduce ProteinWorkshop, a comprehensive benchmark suite for representation learning on protein structures with Geometric Graph Neural Networks. We consider large-scale pre-tr…
RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design
Rishabh Anand, Chaitanya K. Joshi, Alex Morehead +7
We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for dat…
DEFT: Efficient Fine-Tuning of Diffusion Models by Learning the Generalised -transform
Alexander Denker, Francisco Vargas, Shreyas Padhy +7
Generative modelling paradigms based on denoising diffusion processes have emerged as a leading candidate for conditional sampling in inverse problems. In many real-world applicati…
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
Kieran Didi, Francisco Vargas, Simon V Mathis +4
Many protein design applications, such as binder or enzyme design, require scaffolding a structural motif with high precision. Generative modelling paradigms based on denoising dif…
Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?
Charles Harris, Kieran Didi, Arian R. Jamasb +4
Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years.…
On How AI Needs to Change to Advance the Science of Drug Discovery
Kieran Didi, Matej Zečević
Research around AI for Science has seen significant success since the rise of deep learning models over the past decade, even with longstanding challenges such as protein structure…