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DC: Dipolar Coupling Calculations

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For More Information:

DC: Manipulation of Dipolar Couplings
Chemical Shifts, Dipolar Couplings, and Molecular Fragment Replacement
Protein Structure Determination Using Molecular Fragment Replacement and NMR Dipolar Couplings
Molecular Fragment Replacement Approach to Protein Structure Determination
Contacts:
Frank Delaglio     delaglio@nih.gov
Ad Bax     bax@nih.gov

Dipolar Coupling Tensor Analysis by Molecular Fragment Replacement (MFR)

PDB Extended Structure: Input PDB file with an extended structure of the protein. This is used to establish amino acid sequence and atom names. Atom names in the PDB file must exactly match the the names used in the dipolar coupling input. Example: ubiq_ext.pdb
     
   

Dipolar Coupling Input

Dipolar Coupling Input A: Input table of dipolar couplings associated with one alignment medium. The format of the input dipolar coupling table is described in the DC Web Page. Example: dObsA.tab (Neutral Bicelle Sample)
Dipolar Coupling Input B: Optional Input table of dipolar couplings associated with an alternate alignment medium. The format of the input dipolar coupling table is described in the DC Web Page. Example: dObsB.tab (Charged Bicelle Sample)
Dipolar Interaction Values: Keep Existing DI Values Select this option to use existing Dipolar Interaction (DI) values in the DC input tables. Otherwise, DI values will be calculated according to information in the PDB file. In the case of common fixed-geometry peptide couplings (HN-N, HN-C ', N-C ', N-CA, CA - C ', H - CH3 and HA-CA) standardized interatomic distances will be used to calculate DI. Otherwise, atomic distances from the PDB file will be used. If a DI value of 0.0 is specified in the input file, it will always be replaced with a DI value using atomic distances from the PDB file.
     
   

Optional Experimental Data

Shift Input: Optional input table of backbone chemical shifts. Use of chemical shifts can improve the quality of MFR search results. The format of the table is the same as for the TALOS+ software system. Example: ubiq.tab As an alternative, the input table of chemical shifts and sequence information can be specified as a BMRB NMR-Star format file. In order to use NMR-Star format as input for MFR, the BMRB file should have chemical shift information and complete sequence information for a single protein only. When input is supplied as a BMRB file, CYS residues with a CB shift of 34ppm or less are assumed to be reduced, and HIS residues in tables with a listed pH of 6.0 or less are assumed to be protonated. Example: ubiq.str

J-Coupling Input: Optional input table of J-couplings for backbone torsions and their corresponding Karplus parameters. Use of of such J-Coupling values can improve the quality of MFR search results. Example: jcoup.tab
     
   

Graphical Output

Graphical Output: Generate PDF Graphics Select this option to generate graphs of the MFR results in PDF format. Example DC graphics for a protein: dc.pdf Example DC graphics for a small molecule: dcmol.pdf

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