REDCAT: a residual dipolar coupling analysis tool.
Recent advancements in the utilization of residual dipolar couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT's algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.
Valafar
Homayoun
H
Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, GA 30602, USA.
Prestegard
James H
JH
D000465:Algorithms; D001665:Binding Sites; D004151:Dipeptides / Q000032:analysis / Q000737:chemistry; D046911:Macromolecular Substances; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface
D004151:Dipeptides; D046911:Macromolecular Substances