This book constitutes the refereed proceedings of the 6th International Conference on Scalable Uncertainty Management, SUM 2012, held in Marburg, Germany, in September 2012. The 41 revised full papers and 13 revised short papers were carefully reviewed and selected from 75 submissions. The papers cover topics in all areas of managing and reasoning with substantial and complex kinds of uncertain, incomplete or inconsistent information including applications in decision support systems, machine learning, negotiation technologies, semantic web applications, search engines, ontology systems, information retrieval, natural language processing, information extraction, image recognition, vision systems, data and text mining, and the consideration of issues such as provenance, trust, heterogeneity, and complexity of data and knowledge.

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 sites' comparison. In addition, algorithms for the construction of multiple structural alignments are presented as a structural counterpart to multiple sequence alignment. By considering four different types of experiments, namely classification, similarity retrieval, clustering and construction of structural alignments, strengths and weaknesses of the proposed methods are detected and discussed. In addition a hybrid approach is presented which combines the benefits of a feature-based and a geometric method leading to a significant speed-up while still holding very good results.