A unified annotation framework for topological and conformational descriptors is provided and HighDB is compared with representative cyclic peptide resources, showing broader annotation coverage and the largest collection of experimentally resolved cyclic peptide structures among the databases examined.
P PepXPro is presented, a modular framework that transforms publicly available protein-peptide structure-affinity resources into curated datasets and reproducible benchmark collections generated under user-defined criteria that provides an extensible foundation for reproducible protein- peptide benchmark construction.
A redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface that integrates annotation‐, sequence‐, and 3D structure‐based searches, and embeds an interactive 3D viewer.
Yana Rose, Ronald S. Brown, Maria Voigt et al.· Protein Science· 0 citations
Peptide-protein interactions are fundamental to many biological processes, and peptide design is gaining interest due to its therapeutic potential. This has led to the emergence of various structural databases, such as PepBDB and Peptipedia, that classify peptides as polypeptides with fewer than 50 amino acids. These d...
Rahma Hamdani, Javier Delgado, Luis Serrano· Protein Science· 0 citations
HighMorph is presented, an interaction-guided framework that combines protein–protein interaction information with artificial intelligence for rational cyclic peptide design and provides insights for developing therapeutics targeting challenging protein interfaces.
M. Lan, Cheng-Yun Zhang, Wentong Wang et al.· Journal of Medicinal Chemist...· 0 citations
Structure-based drug design (SBDD) models are central to modern pharmaceutical research, enabling the rational exploration of protein-ligand interactions at atomic resolution. However, most existing approaches frame molecular generation as an isolated optimization or a one-to-one matching task, overlooking the shared b...
Dong Xu, Zhang-Fan Yang, Junchuang Cai et al.· IEEE transactions on computa...· 1 citation
Scop3P-Toolkit is an open-source executable analytical environment for interactive analysis of PTMs, mutations, and proteomics-derived peptides in their structural context, providing transparent, accessible, and reproducible workflows for both computational and experimental researchers.
Adrián Díaz, Natalia Tichshenko, Boris Depoortere et al.· bioRxiv· 0 citations
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