Abstract
Adeno-associated virus (AAV) capsid engineering is essential for advancing gene therapy but remains limited by structural complexity and computational constraints. To address these challenges, we developed CapBuild, a cloud-native web server that streamlines AAV capsid prediction, assembly and engineering. CapBuild provides two distinct workflows: a PDB-based pipeline for assembling complete capsids from structural files and a modelling pipeline that constructs capsids from protein sequences via SWISS-MODEL. The platform incorporates icosahedral symmetry through transformation matrices and features an integrated mutation modeller for visualising site-specific mutations across the entire capsid. Additionally, its amino acid localisation tool maps exposed and buried residues, facilitating rational design. Benchmarking against crystal structures demonstrates high structural accuracy, with consistently low RMSD values (0-0.89 Å) and high GDT scores (89.4-100%) across multiple AAV serotypes. CapBuild's interactive visualisation interface, powered by Mol*, enables in-depth structural analysis, making capsid engineering more accessible to researchers. By reducing technical barriers and automating complex modelling tasks, CapBuild facilitates early-stage AAV capsid design, enabling researchers to rationally explore and visualise structural variants for potential use. CapBuild is available at https://capbuild.csiro.au/.