Evolution and physics in comparative protein structure modeling.
From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.
Fiser
András
A
Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
Feig
Michael
M
Brooks
Charles L
CL
Sali
Andrej
A
D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D019143:Evolution, Molecular; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins