Kasra Manavi, Alan Kuntz and Lydia Tapia Geometrical Insights into the Process of Antibody Aggregation AAAI Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, July 2013 IgE antibodies bound to cell-surface receptors, FceRI, crosslink through the binding of antigens on the cell surface. This formation of aggregates is what stimulates mast cells and basophils in order to initiate degranulation, resulting in an allergic response. Nearly 1,500 Americans die each year from anaphylactic shock predicated by aggregation. Experimental studies have shown the spatial orga- nization of the aggregated IgE-FceRI complexes affect transmembrane signaling that initiates allergic response. There are many factors that can affect the shapeand size of aggregates. However, one critical factor maybe the conformational structure of the antigen (ligand).This structure can affect the number of receptors that can bind to a single ligand, e.g., the valency of the ligand. For example, a common hay fever antigen has avalency of four where as the common shrimp antigenhas a valency of eighteen. 3-D simulation of hundreds of antibodies aggregating can be computationally infeasible. However, we present methods based on robotic representations of molecular structures and Monte Carlo simulation that provide 3-D details of aggregate formation. In this paper, we demon- strate the utility of our methods on ligands of different valences: a bivalent DCT2-cys (DCT) and a trivalent fibritin trimer (DF3). We show that we can capture ex- perimentally measured properties while enabling a de- tailed look into the geometry of aggregation formation.