Why The hausse of molecular biology and structural biology has caused an exponential growth of available 3D structures of macromolecules. However, there are still many more proteins without than with elucidated structure. With the Human Genome project well on their way, we need fast methods for reliable protein structure prediction based on the genetic code alone. A reliable structure could, even more than a sequence, help in understanding what kind of protein has been found to be coded in the genome.
Most programs only recognize disulfide bridges and no other motifs.
Check the amount of residues visually and the secondary structure of their source as well as the check for steric clashes with SCRs and bad disulfide contacts. In case of superb homology, the backbone should not be minimised. The resulting structure could pass all checks. There are some Internet homology modelling services. This can be handy, but remember that all models are useful, not necessarily true.