title: Geometry of protein shape and its evolutionary pattern for function prediction and characterization.
abstract: Proteins contain thousands or more atoms and have complex shapes. We discuss here the computation of protein packing defects, in the form of voids and pockets, from experimentally resolved protein structures, and the nature of their distribution and scaling behavior, as well as their origin. We further discuss how evolutionary selection pressure due to biological function unaltered by selection pressure due to constraints from folding and stability can be isolated and estimated, and how such information can be used to predict protein function and characterize binding properties of enzymes.
authors: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA. jliang@uic.edu
authors: Jie
authors: J
authors: Liang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D008962:Models, Theoretical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins