Résumé
HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T1/T2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 A and 3.8 A with a distribution centered at 3.3 A. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures. If the average structure is correct, deviations between experimental T1/T2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.