Computational techniques for efficient conformational sampling of proteins.
In this review, we summarize the computational methods for sampling the conformational space of biomacromolecules. We discuss the methods applicable to find only lowest energy conformations (global minimization of the potential-energy function) and to generate canonical ensembles (canonical Monte Carlo method and canonical molecular dynamics method and their extensions). Special attention is devoted to the use of coarse-grained models that enable simulations to be enhanced by several orders of magnitude.
Liwo
Adam
A
Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, United States.
Czaplewski
Cezary
C
Ołdziej
Stanisław
S
Scheraga
Harold A
HA
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D011506:Proteins