Coarse-grained simulations of protein aggregation.
Protein aggregation is believed to be responsible for a number of human diseases and limits the yields of pharmaceutical proteins during production. Computer simulations can be used to develop novel experimentally testable hypotheses pertaining to aggregation. While all-atom simulations with explicit solvent are too computationally intensive to address the multitude of relevant time scales, coarse-grained models make it possible to observe the transition of monomers to an equilibrium containing aggregates. Here, we provide the reader with background information and a list of steps for setting up, performing, and analyzing computer simulations of aggregating coarse-grained (CG) proteins.
Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA. cellmert@niddk.nih.gov
Troy
T
Cellmer
Nicolas L
NL
Fawzi
D000465:Algorithms; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
D011506:Proteins; D012997:Solvents