Modeling of folds and folding pathways for some protein families of (α + β)- and (α/β)-classes

Abstract

In this paper, updated structural trees for α/β-proteins containing five- and seven-segment (α/β)-motifs are represented. Novel structural motifs occurring in some families of (α + β)- and (α/β)-proteins are also characterized. Databases of these proteins have been compiled from the Protein Data Bank (PDB) and Structural Classification of Proteins (SCOP) and the corresponding structural trees have been constructed. The classification of these proteins has been developed and organized as an extension of the PCBOST database, which is available at http://strees.protres.ru. In total, the updated Protein Classification Based on Structural Trees database contains 11 structural trees, 106 levels, 635 folds, 4911 proteins and domains, and 14,202 PDB entries.

Keywords:

• structural motif
• handedness
• structural tree
• classification

Acknowledgments

This work was supported by the Russian Foundation for Basic Research (Project No. 10-04-00727).