PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides

In recent years, the development of peptide drugs has seen significant growth. These molecules often go beyond simple linear chains composed of the standard 20 amino acids. Peptide drugs frequently incorporate non-standard amino acids, non-amino components, and can exhibit mono- or multicyclic structures, branching, and other complex topologies. Consequently, there is a growing need for accessible tools that allow researchers to easily generate and modify 1D, 2D, and 3D representations of these complex peptides, serving as a starting point for further optimization. PEP-EDIT was created to meet this need. It offers a user-friendly, interactive web interface for generating complex peptide representations from 1D BILN (Boehringer Ingelheim Line Notation) sequences, using a customizable monomer library. Building on the pyPept library, PEP-EDIT enhances its functionality with options such as pH-dependent protonation and simplified specification of conformational constraints. The platform leverages interactive 2D and 3D visualizations to guide peptide design, offers intuitive management of monomers and 3D models, and includes collaborative and interactive visualization tools. PEP-EDIT is available at https://pep-edit.rpbs.univ-paris-diderot.fr. This website is free and open to all users and there is no login requirement.