The modeling of loops remains a challenging theoretical and practical problem in the prediction of protein structure (1). There are several general methods for modeling such loops including the use of databases (2–5), simulation (6–8), and ab initio methods (9–10) as well as other methods described in this volume. In this chapter, an ab initio method is described that uses conformational search to thoroughly explore the possible conformations of a loop, and that uses an energy function to rank this conformations for the prediction of the loop. In addition, a detailed protocol for homology modeling using the program, CONGEN, will be presented along using an example taken from the recent Comparative Assessment of Structural Prediction 2 (CASP2).