Protein aggregation is a major hurdle in the development and manufacturing of protein-based therapeutics. The development of aggregation-resistant and stable protein variants can be guided by rational redesign using computational tools. Here, we describe the architecture and functionalities of the Aggrescan3D (A3D) standalone package for the rational design of protein solubility and aggregation properties based on three-dimensional protein structures. We present the case studies of the three therapeutic proteins, including antibodies, exploring the practical use of the A3D standalone tool. The case studies demonstrate that protein solubility can be easily improved by the A3D prediction of non-destabilizing amino acid mutations at the protein surfaces.