Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding prote

Background: When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results: The precomputed Magnum database offers a solution to this problem for ca. 1,800 fulllength protein families with at least one crystal structure. The Magnum deliverables include 1) multiple sequence alignments, 2) mapping of alignment sites to crystal structure sites, 3) phylogenetic trees, 4) inferred ancestral sequences at internal tree nodes, and 5) amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accu...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Michael E. Bradley, Steven A. Benner
• Keywords: Accurate Models, BMCBI 2006, Protein, Protein Structures