A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provisions for redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross-reactions.