hm-benchmark

All are not equal: A benchmark of differenthomology modeling programsBJÖRN WALLNER AND ARNE ELOFSSONStockholm Bioinformatics Center, Albanova University Center, Stockholm University, Stockholm, Sweden(RECEIVED November 22, 2004; FINAL REVISION February 18, 2005; ACCEPTED February 18, 2005)AbstractModeling a protein structure based on a homologous structure is a standard method in structural biologytoday. In this process an alignment of a target protein sequence onto the structure of a template(s) is usedas input to a program that constructs a 3D model. It has been shown that the most important factor in thisprocess is the correctness of the alignment and the choice of the best template structure(s), while it isgenerally believed that there are no major differences between the best modeling programs. Therefore, alarge number of studies to benchmark the alignment qualities and the selection process have been performed.However, to our knowledge no large-scale benchmark has been performed to evaluate the programs used totransform the alignment to a 3D model. In this study, a benchmark of six different homology modelingprograms— Modeller, SegMod/ENCAD, SWISS-MODEL, 3D-JIGSAW, nest, and Builder—is presented.The performance of these programs is evaluated using physiochemical correctness and structural similarityto the correct structure. From our analysis it can be concluded that no single modeling program outperformthe others in all tests. However, it is quite ...