LinkCraft: An interactive tool for the design of flexible linkers

Multi-domain proteins connect functional domains through flexible linkers that critically determine their spatial arrangement and cooperative behavior. Most inter-domain linkers are intrinsically disordered regions (IDRs), whose conformational flexibility is essential for function. The design of such multimodular proteins is becoming increasingly important in biotechnology and synthetic biology, where engineered assemblies combine catalytic, regulatory, or binding domains to create systems with desired functionalities. However, although domain engineering is now well established, rational linker design remains challenging because linker properties depend on multiple coupled factors, including sequence composition, charge patterning, and length. Here, we present LinkCraft, a computational tool for the rational design of intrinsically disordered linkers (IDLs) in multi-domain proteins. LinkCraft suggests a range of suitable IDL lengths as a function of the inter-domain distance and supports custom linker sequence definition or sequence generation based on desired physicochemical properties. The ensemble-based modeling of the designed multi-modular protein enables users to evaluate linker behavior and dynamics within its structural context. The tool provides an easy-to-use framework for prototyping complex protein constructions, promoting a shift from domain-centric to multi-modular-centric protein design, where linkers are treated as active, tunable determinants of molecular function. LinkCraft is freely available at https://gitlab.laas.fr/moma/binaries/linkcraft/.