Experimental restraints in the energy function

Post, C. B.; Dadarlat, V. M.

doi:10.1107/97809553602060000706

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 20.2, pp. 490-491 | 1 | 2 |

Section 20.2.3.3. Experimental restraints in the energy function

C. B. Post^a ^* and V. M. Dadarlat^a

^aDepartment of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907-1333, USA
Correspondence e-mail: cbp@cc.purdue.edu

20.2.3.3. Experimental restraints in the energy function

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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, $[E_{\rm tot} = E_{\rm empir} + E_{\rm rest}]$ . 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, $[E_{\rm rest} = wE_{\rm Xray}]$ , the residual between the observed and calculated structure-factor amplitudes; where $[wE_{\rm Xray} = w\textstyle\sum\limits_{hkl}\displaystyle \left(\left|F_{o} \right| - k\left| F_{c} \right| \right)^{2},]$ where w and k are scale factors.

References

International Tables for Crystallography (2006). Vol. F. ch. 20.2, pp. 490-491