Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility. A3D allows the re-design of protein solubility by combining structural aggregation propensity and stability predictions, as demonstrated by a recent experimental study. It also enables predicting the impact of protein conformational fluctuations on the aggregation properties. The standalone A3D version is an upgrade of the original web server implementation-it introduces a number of customizable options, automated analysis of multiple mutations and offers a flexible computational framework for merging it with other computational tools.