Diffusion-collision model algorithms for protein folding kinetics.
The diffusion-collision model (DCM) of protein folding is described qualitatively and quantitatively. The input parameters required to perform a calculation are explained, and the output data are outlined. Three examples are given of calculating DCM folding kinetics: the Engrailed Homeodomain (a three-helix bundle with three helical microdomains, pdb code 1ENH), protein G (with three microdomains having a beta-hairpin-alpha-helix-beta-hairpin motif, pdb code 1PGA), and apomyoglobin (with eight helices and seven strong microdomain-microdomain pairings).
Vasilkoski
Zlatko
Z
Molecular Modeling Laboratory, Department of Physics, Tufts University, Medford, Massachusetts 02155, USA.
Weaver
David L
DL
D000465:Algorithms; D001059:Apoproteins / Q000737:chemistry; D003198:Computer Simulation; D004058:Diffusion; D007074:Immunoglobulin G / Q000737:chemistry; D007700:Kinetics; D008962:Models, Theoretical; D009211:Myoglobin / Q000737:chemistry; D017510:Protein Folding
D001059:Apoproteins; D007074:Immunoglobulin G; D009211:Myoglobin; C010857:apomyoglobin