Target-Specific Peptide Binder Design with DiffPepBuilder.

Despite the exciting progress in target-specific protein binder design, peptide binder design remains challenging due to the flexibility of peptide structures and the scarcity of protein-peptide complex structure data. In this study, we curated a large synthetic data set, referred to as PepPC-F, from the abundant protein-protein interface data and developed DiffPepBuilder, a target-specific peptide binder generation method that utilizes an SE(3)-equivariant diffusion model trained on PepPC-F to codesign peptide sequences and structures. DiffPepBuilder also introduces disulfide bonds to stabilize the generated peptide structures.

SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration.

In this work, we introduced a siderophore information database (SIDERTE), a digitized siderophore information database containing 649 unique structures. Leveraging this digitalized data set, we gained a systematic overview of siderophores by their clustering patterns in the chemical space. Building upon this, we developed a functional group-based method for predicting new iron-binding molecules with experimental validation.

The Overexpression of Strigolactone Receptor Gene Enhances Drought Resistance in L.

Strigolactones (SLs) represent a recently identified class of plant hormones that are crucial for plant tillering and mycorrhizal symbiosis. The gene, an essential receptor within the SLs signaling pathway, has been well-examined in crops, like rice ( L.) and ( L.

Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models.

A persistent goal for drug design is to generate novel chemical compounds with desirable properties in a labor-, time-, and cost-efficient manner. Deep generative models provide alternative routes to this goal. Numerous model architectures and optimization strategies have been explored in recent years, most of which have been developed to generate two-dimensional molecular structures.