2025年5月27日 · By employing explicit all-atom and bond modeling, CpSDE overcomes existing data limitations and is proficient in designing a wide variety of cyclic peptides. Our experimental results …

To address the above challenges, we introduce CpSDE, which consists of two key components: AtomSDE, a generative structure prediction model based on harmonic SDE, and ResRouter, a …

Here, we introduce AfCycDesign, a deep learning approach for accurate structure prediction, sequence redesign, and de novo hallucination of cyclic peptides. Using AfCycDesign, we identified over …

2025年5月21日 · Here, we introduce AfCycDesign, a deep learning approach for accurate structure prediction, sequence redesign, and de novo hallucination of cyclic peptides. Using AfCycDesign, …

We argue that the core ratio clipping mechanism in PPO is structurally ill-suited for the large vocabularies inherent to LLMs. PPO constrains policy updates based on the probability ratio of …

2025年6月18日 · Although deep generative models have achieved great success in linear peptide design, several challenges prevent the development of computational methods for designing diverse …

2025年4月30日 · Current FDA approved cyclic peptide-based drugs are mostly derived from natural sources. However, recent work has enabled the computational design of new cyclic peptide drugs.

Abstract Cyclic peptides exhibit better binding affinity and proteolytic stability compared to their linear counterparts. However, the development of cyclic peptide de-sign models is hindered by the …

2025年12月17日 · PXDesign is a model suite for de novo protein-binder design — a diffusion generator (PXDesign-d) paired with Protenix and AF2-IG confidence models for selection. Across seven …

2024年12月2日 · In this study, we modified the powerful RFdiffusion model to allow the cyclic peptide structure identification and integrated it with ProteinMPNN and HighFold to design binders for …