LPFC: an Internet library of protein family core structures

As the number of protein molecules with known, high-resolution structures increases, it becomes necessary to organize these structures for rapid retrieval, comparison, and analysis. The Protein Data Bank (PDB) currently contains nearly 5,000 entries and is growing exponentially. Most new structures are similar structurally to ones reported previously and can be grouped into families. As the number of members in each family increases, it becomes possible to summarize, statistically, the commonalities and differences within each family. We reported previously a method for finding the atoms in a family alignment that have low spatial variance and those that have higher spatial variance (i.e., the "core" atoms that have the same relative position in all family members and the "non-core" atoms that do not). The core structures we compute have biological significance and provide an excellent quantitative and visual summary of a multiple structural alignment. In order to extend their utility, we have constructed a library of protein family cores, accessible over the World Wide Web at http:/ /www-smi.stanford.edu/projects/helix/LPFC/. This library is generated automatically with publicly available computer programs requiring only a set of multiple alignments as input. It contains quantitative analysis of the spatial variation of atoms within each protein family, the coordinates of the average core structures derived from the families, and display files (in bitmap and VRML formats). Here, we describe the resource and illustrate its applicability by comparing three multiple alignments of the globin family. These three alignments are found to be similar, but with some significant differences related to the diversity of family members and the specific method used for alignment.