MBA:
Model-Based Assignment


A software for inferential assignment of protein
backbone nuclear magnetic resonances

 

Home

Installation

Input files

Execution

Output

Convergence

Input files:

To facilitate comparison between tools, MBA supports an input format that is similar to the format of program MARS. MBA requires 4 input files:

1. File containing parameter settings
2. File containing a list of pseudoresidues and their chemical shifts
3. File containing the primary sequence of the protein
4. File containing a predicted secondary structure of the protein

 

Below is an example of the parameter setting file mba.inp

 cutoffCO:     0.25			# Connectivity cutoff (ppm) of CO [0.25]
 cutoffCA:     0.5			# Connectivity cutoff (ppm) of CA [0.5]
 cutoffCB:     0.5			# Connectivity cutoff (ppm) of CB [0.5]
 cutoffHA:     0.25			# Connectivity cutoff (ppm) of HA [0.25]

 sequence:     1ubq_fasta.tab		# Primary sequence (FASTA format)
 secondary:    1ubq_psipred.tab		# Secondary structure (PSIPRED format)
 csTab:        1ubq_cs.tab		# Chemical shift table

 hasReference: YES			# Chemical shift table contains reference [NO]
The difference between formats for MARS and MBA is that MBA does not make use of the protein's 3D structure or of experimental RDCs. It is possible to use a complete input file from MARS as input for MBA, the lines that are not used will be ignored.

The last line of the file is optional and specifies whether the table of chemical shifts contains a reference assignment obtained by an alternative method. The reference assignment will not be used by MBA, but the output will provide a comparison between solutions.

Please refer to the MARS web page for the formats of the other input files. To specify a reference assignment name pseudoresidues in the table of chemical shifts according to their position in the sequence. The names must be numeric and contain no characters.