A union of sequence-structure analysis with character-based tree-building methods will create new opportunities for hypothesis testing that have the potential to further enhance the use of a sequence-structure approach in standard phylogenetic analyses, as well as, for DNA barcoding.
Two distinct characters of ADAM are its size and sequence-structure analysis.
To understand the basis for the functional versatility of this small fold we undertook a comprehensive sequence-structure analysis of the fold and developed a natural classification for its members.
Author response: While we fully understand the sentiment and agree that the hypothesis on prokaryotic RNAi is of greater general interest than the detailed presentation of the protein sequence-structure analysis, we strongly feel that the latter provides a badly needed foundation for the hypothesis as well as important information in its own right.
This is a fascinating insight, based on sequence and structure analysis alone, and illustrates how careful sequence searches and information from structural genomics can suggest functions for uncharacterized proteins.
We envision that the 3DSwap knowledgebase and its features, such as integrated visualization tools and the various sequence and structure analysis results, will benefit the structural bioinformatics community, and enable researchers to perform comprehensive analysis and classification of proteins involved in 3D domain swapping.
We assessed the homology-detection effectiveness of these methods using search results for the ASTRAL Compendium for Sequence and Structure Analysis [ 30] and the Structural Classification of Proteins (SCOP) [ 31] databases.
These rules were incorporated into an N-linked glycosylation prediction tool: Sequence Structure Feature Analysis Tool (SFAT).
Alva, V., Nam, S. Z., Söding, J. & Lupas, A. N. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.
Adekoya, O. A., Helland, R., Willassen, N. P. & Sylte, I. Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family.
