bioRxiv Science⌕ Search

Biology subjects

Boyd, N.

Publications and source records attributed to Boyd, N..

3 recordsLinked to original sources

Drug-like antibody design against challenging targets with atomic precision

Computational antibody design has seen rapid progress, with high success rates enabling direct translation to characterization without any high-throughput screening required. In this work, we markedly expand the scope of de novo antibody design by applying our state-of-the-art Chai-2 platform to design drug-like antibodies in full-length monoclonal format. We find that >86% of these full-length mAbs have strong developability profiles on par with therapeutic antibodies. We further show that experimentally determined structures of Chai-2 designs closely match their in silico predictions, demonstrating that Chai-2 produces atomically accurate models of designed antibodies. Building on these foundational capabilities, we showcase two potential applications of Chai-2 against different targets: designing functional antibodies mediating GPCR agonism, and highly specific antibodies selectively binding tumor-specific neoepitopes. Taken together, this work brings new flexibility to modern discovery pipelines, accelerating the path from in silico design to functional validation across both conventional and challenging targets. Beyond reducing the cost and timelines associated with large screening campaigns, in silico design can now open new frontiers for creative, targeted therapeutics that address unmet clinical needs.

molecular biology↗

ATOM-1: A Foundation Model for RNA Structure and Function Built on Chemical Mapping Data

RNA-based medicines and RNA-targeting drugs are emerging as promising new approaches for treating disease. Optimizing these therapeutics by naive experimental screening is a time-consuming and expensive process, while rational design requires an accurate understanding of the structure and function of RNA. To address this design challenge, we present ATOM-1, the first RNA foundation model trained on chemical mapping data, enabled by data collection strategies purposely developed for machine learning training. Using small probe neural networks on top of ATOM-1 embeddings, we demonstrate that this model has developed rich internal representations of RNA. Trained on limited amounts of additional data, these small networks achieve state-of-the-art accuracy on key RNA prediction tasks, suggesting that this approach can enable the design of therapies across the RNA landscape.

bioinformatics↗

DeepLoco: Fast 3D Localization Microscopy Using Neural Networks

Single-molecule localization super-resolution microscopy (SMLM) techniques like STORM and PALM have transformed cellular microscopy by substantially increasing spatial resolution. In this paper we introduce a new algorithm for a critical part of the SMLM process: estimating the number and locations of the fluorophores in a single frame. Our algorithm can analyze a 20000-frame experimental 3D SMLM dataset in about one second -- substantially faster than real-time and existing algorithms. Our approach is straightforward but very different from existing algorithms: we train a neural network to minimize the Bayes risk under a generative model for single SMLM frames. The neural network maps a frame directly to a collection of fluorophore locations, which we compare to the ground truth using a novel loss function. While training the neural network takes several hours, it only has to be done once for a given experimental setup. After training, localizing fluorophores in new images is extremely fast -- orders of magnitude faster than existing algorithms. Faster recovery opens the door to real-time calibration and accelerated acquisition, and future work could tackle more complicated optical systems and more realistic simulators.

biophysics↗