We develop new methods for learning the structures of proteins and other molecules that play central roles in human disease. We apply these methods to specific problems where more conventional methods are not adequate. As an example, we developed detailed models of amyloid fibrils. Amyloid fibrils may be linked to Alzheimer's disease and type 2 diabetes. Our models reveal the molecular interactions that lead to amyloid fibrils. This knowledge will inform the design of chemical compounds to inhibit fibril formation.