Fast method for estimating the energy distribution of globular states of proteins.
By an enumeration study, we show that the energy distributions of a lattice protein sequence on all possible compact lattice configurations can be approximated by the energy distribution of shuffled sequences on a given lattice structure. We also show that the random energy model (REM) gives a good analytical approximation for the energy distribution of shuffled sequences on lattice structures. For real proteins, when a gapped threading method is used, REM calculations systematically underestimate the mean value of the energy distributions. We found that this discrepancy can be roughly compensated by a linear correction obtained from empirical fits. This result can be used to greatly reduce the computational effort in protein threading calculations.
Cao
Hai-Bo
HB
Department of Physics and Astronomy, Ames Laboratory-U.S. DOE, Iowa State University, Ames, Iowa 50011, USA.
Wang
Cai-Zhuang
CZ
Ho
Kai-Ming
KM
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins