The structural comparison of whole proteins or protein binding sites is usually performed by making use of graphs. Even though graphs exhibit a lot of interesting and useful properties, the usage of other representations can come along with several benefits. In this book the representation of a protein binding site is tackled. Three representations are considered namely the geometric, the feature-based and the graph-based representation. For all three types, some completely new algorithms are developed and presented. Moreover, existing methods are adapted to the application of protein binding...

Constitutes the refereed proceedings of the 6th International Conference on Scalable Uncertainty Management, SUM 2012, held in Marburg, Germany, in September 2012.