Most of the examples listed can be traced in the literature. Certainly not, the pitfalls listed could have been avoided. Understanding the limitations of tools is almost the entire way to a successful application. Theoretical biology still fails to predict 3D structure from sequence, but predictions of various simplified 1D aspects of structure become more accurate and more useful with every new sequence added to public databases. Bridging the protein sequence-structure gap by structure predictions.
Protein fold recognition.
The relation between the divergence of sequence and structure in proteins.