DYANA

Giintert P, Mumenthaler C, Wiithrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997 273 283-298. 

The key idea of the fast torsion angle dynamics algorithm in Dyana is to exploit the fact that a chain molecule such as a protein or nucleic acid can be represented in a natural way as a tree structure consisting of n+1 rigid bodies that are connected by n rotatable bonds (Fig. 2.1) [74, 83]. Each rigid body is made up of one or several mass points (atoms) with invariable relative positions. The tree structure starts from a base, typically... 

The role of the potential energy is taken by the Dyana target function [8, 28] that is defined such that it is zero if and only if all experimental distance constraints and torsion angle constraints are fulfilled and all nonbonded atom pairs satisfy a check for the absence of steric overlap. A conformation that satisfies the constraints more closely than another one will lead to a lower target function value. The exact definition of the Dyana target function is ... 

Perform structure calculation using DYANA torsion angle dynamics... 

The core of the current version of Candid is implemented in standard Fortran-77 and has been built upon the data structures and into the framework of the user interface of the program Dyana. The standard schedule and parameters for a complete automated structure determination with Candid and Dyana are specified in a script written in the interpreted command language Inclan that gives the user high flexibility in the way automated structure determination is performed without the need to modify the compiled core part of Candid [26]. 

Fig. 5.6 Superposition of the backbone representation of the 20 lowest energy DYANA structures of NPY/DPC.

Two programs, CNS (Crystallography and NMR system)214 and DYANA (dynamics algorithm for NMR applications),215 are widely used for refining... 

NMR constraints are molecular mechanics force fields like DYANA. It was... 

Residual value of the DYANA target function (Giintert et al, 1997) before energy minimization for an individual calculation a small value indicates good convergence. 

Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319 209-227... 

For the interpretation of the experiments the follo dng codes were used TRIO-DYN, ATTICA-DYANA, FLUTAN, ASTEC. Accompanying in-pile tests have been performed in PHENIX and SUPERPHENIX [5.36,5.37]. 

---