Efficient sampling of protein structures by model hopping.
We introduce a novel simulation method, model hopping, that enhances sampling of low-energy configurations in complex systems. The approach is illustrated for a protein-folding problem. Thermodynamic quantities of proteins with up to 46 residues are evaluated from all-atom simulations with this method.
Kwak
Wooseop
W
Department of Physics, Michigan Technological University, Houghton, Michigan 49931-1295, USA. wkwak@mtu.edu
Hansmann
Ulrich H E
UH
D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013205:Staphylococcal Protein A / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
D011506:Proteins; D013205:Staphylococcal Protein A