Structure generation engines

CNS (Crystallography and NMR system) is the structure generation engine, on which ARIA was developed and is currently based. CNS has been designed to provide a flexible multi-level hierarchical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include several crystallographic refinement methods, as well as NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. The reference describing CNS is:

AT Brünger, PD Adams, GM Clore, WL DeLano, P Grose, RW Grosse-Kunstleve, JS Jiangf, J Kuszewskic, M Nilges, NS Pannuh, RJ Readi, LM Rice, T Simonson, and GL Warren. Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination (1998) Acta Cryst. D54, 905-921. Pubmed

CNX( @ Accelrys) is an integrated software package that provides a one-stop solution of validated science for crystallographers. It is based on the widely used programs X-PLOR and CNS, but extends the capabilities of these programs and offers functionality that can significantly increase the speed of the structure solution process. Most of the functionnalities of ARIA should be available using CNX.

CYANA Combined assignment and dynamics algorithm for NMR applications (© by Peter Güntert) is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. The combination of automated NOESY cross peak assignment, structure calculation with a fast torsion angle dynamics algorithm, and the ease-of-use of CYANA provide for unprecedented efficiency in NMR protein structure determination. The reference describing CYANA is:

Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA.(1997) J. Mol. Biol. 273, 283-298. Pubmed

XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH. These tools include several specific NMR, solution X-ray and neutron scaavailable inttering functionalities. XPLOR-NIH also includes an new internal variable module (IVM) which allows one to perform efficient molecular dynamics and minimizations using internal coordinates, such as torsion angles. The IVM permits one to do combined torsion angle/rigid body dynamics, torsion angle/cartesian coordinate dynamics, etc. The reference describing XPLOR-NIIH is:

C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore. The Xplor-NIH NMR Molecular Structure Determination Package (2003) J. Magn. Res., 160, 66-74. Pubmed