The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules.

ABSTRACT: Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force field

SUBMITTER: Sproviero EM 

PROVIDER: S-EPMC2954272 | biostudies-literature | 2009 Nov-Dec

REPOSITORIES: biostudies-literature