Shape analysis plays an important role in many applications. In particular, in molecular biology, analyzing molecular shapes is essential to the fundamental problem of understanding how molecules interact. This project aims at developing efficient and effective algorithms to characterize and analyze molecular structures using geometric and topological methods. Two main components of this project are (1) developing novel molecular shape descriptors; and (2) identifying and representing meaningful features based on those descriptors. The project also produces accompanying (visualization) software. Results from this project (09/2006–10/2009) include the following publications. We have also set up web-servers for the software developed in this period, so that our new methods are accessible to a broader scientific community. The web sites are given below as well. In this final technical report, we first list publications and software resulted from this project. We then briefly explain the research conducted and main accomplishments during the period of this project.