title: A global representation of the protein fold space.
abstract: One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the "protein structure universe." Here, we present a 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable. The shape of the fold space and the overall distribution of the folds are defined by three dominant trends: secondary structure class, chain topology, and protein domain size. Random coil-like structures of small proteins and peptides are mapped to a region where the three trends converge, offering an interesting perspective on both the demography of fold space and the evolution of protein structures.
authors.affiliation: Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
authors.forename: Jingtong
authors.initials: J
authors.lastname: Hou
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Sims
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.forename: Sung-Hou
authors.initials: SH
authors.lastname: Kim
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D055592:Biophysical Phenomena; D001703:Biophysics; D008958:Models, Molecular; D010802:Phylogeny; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D011506:Proteins