This document deals with the various aspects of molecular modeling of a protein in the extracellular matrix. In this work the thrombospondin signature domain is studied in detail, using various methods from different fields of science. Due to the complexity of the protein, a classical molecular dynamics and a quantum molecular approach is chosen to gain insights into the thrombospondin signature domain. During this process a new algorithm that allows to derive partial charges from ab-initio calculations has been developed. In order to run this algorithm in an efficient way new programming techniques, such as massive multiparallel programming on graphics processors has been used. Further new visualization methods have been either tried or developed effectively generating a new kind of art from the scientific results that have been obtained in this project. Besides these developments several interesting insights into the dynamics of thrombospondins have been revealed. We were able to identify the exchangeable ions within the thrombospondin signature domain, and were further capable to verify and extend existing models for a low calcium signature domain structure. Binding sites important for cancer drug design have also been evaluated using the molecular dynamics simulations.
