BMRZ Webportal
MARS
MARS Webportal

MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity to large proteins and those with very high degeneracy such as partially or fully unfolded proteins. The program does not require tight adjustment of thresholds for establishing the sequential connectivity. MARS works with a wide variety of NMR experiments and is robust against missing or erroneous chemical shift information. In case of a known 3D structure, residual dipolar couplings can be used to enhance assignment. The results can be used directly with the program SPARKY to allow visual validation of the assignment. Thus, several cycles of automatic assignment using MARS and manual validation can be performed, in order to complete assignment even in difficult cases. The MARS software, as implemented in the webportal was kindly provided by Markus Zweckstetter.

One can use a tool to merge two chemical shift tables.


Input parameters
Is the protein perdeuterated ?No  Yes
Is the protein disordered (unfolded) ?No  Yes
Are oxidized cysteins present ?No  Yes, residues (comma separated) :

Max. length of pseudoresidue fragments : Required! Invalid Format! Invalid Range (3-7) ! Invalid Range (3-7) !
Connectivity cutoff for CO (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for CA (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for CB (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for HA (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for HN (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for N (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for HN+1 (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !
Connectivity cutoff for N+1 (in ppm) : Required! Invalid Format! Invalid Range (0.01-2 ppm) ! Invalid Range (0.01-2 ppm) !

Input files
Chemical shift table (csTab) : Required!
Secondary structure (PSIPRED) : Required!
Primary sequenced (FASTA) : Required!

Optional
Fixing sequential connectivity (fixConn) :
Fixing residue type and/or assignment (fixAss) :
Chemical shift prediction (csPred-Manual) :
Scalar couplings (PALES, jcTab) :
Residual Dipolar couplings (PALES, dcTab) :
RDCs for exhaustive SVD (PALES, dObsExh) :
3D structure file (PDB with hydrogens) :
3D structure resolution (Angstrom) : Invalid Format!
Method for obtaining the alignment tensor :Grid search  Single value decomposition (SVD)
Exhaustive back-calculation SVD  Shape prediction
Iterations for aligment tensor refinement : Invalid Format! Invalid Range (2,3 or 4) ! Invalid Range (2,3 or 4) !

Job Submission
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