Computing conformational free energy by deactivated morphing.
Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called "deactivated morphing," in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.
Park
Sanghyun
S
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA. sanghyun@mcs.anl.gov
Lau
Albert Y
AY
Roux
Benoît
B
D000409:Alanine / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D004151:Dipeptides; D014867:Water; D000409:Alanine