International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 20.2, pp. 490-491
Section 20.2.3.3. Experimental restraints in the energy function
aDepartment of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907-1333, USA |
For the purpose of structure determination, the potential-energy function used for molecular-dynamics calculation incorporates the information from experimental data in the form of non-physical restraint terms. These restraint terms, introduced to bias the conformational sampling toward structures consistent with the experiment, are used in addition to the total potential function and, in some sense, can fulfil the requirements of a physical term in equation (20.2.2.2) (see below). The experimentally based restraint terms are added to the potential-energy function to give a total effective potential, . Whereas structure-determination protocols based on NMR data employ a number of types of restraint terms, data from X-ray crystallography provide a single restraint term, , the residual between the observed and calculated structure-factor amplitudes; where where w and k are scale factors.