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DC: Servers for Dipolar Coupling Calculations

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See Also:

About DC: Server-Based Tools for Dipolar Coupling Calculations
Chemical Shifts, Dipolar Couplings, and Molecular Fragment Replacement
NMR Server PDB Utilities to Add Protons, Align Structures, etc
NMRPipe Table Format
Contacts:
Frank Delaglio     delaglio@nih.gov
Ad Bax     bax@nih.gov

DC Order Matrix Fitting: Fit Dipolar Couplings to a PDB Structure Using SVD

This server provides a simple fit of an existing set of dipolar couplings to an existing structure. It uses the Order Matrix method of fitting the couplings via Singular Value Decomposition (SVD). It returns the couplings predicted by the fit, and the parameters of the alignment tensor determined by the fit. The server also includes various options for error analysis and cross-validation.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/svd.html

Restrained Fit of Dipolar Couplings to a PDB Structure Using Non-Linear Least Squares

This server provides a restrained fit of an existing set dipolar couplings to an existing structure. It returns the couplings predicted by the fit, and the parameters of the alignment tensor determined by the fit. In the restrained fit, it is possible to select upper and lower limits or fixed values for the tensor magnitude, rhombicity, and orientation angles. The server also includes various options for error analysis and cross-validation.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/fit.html

Calculate Specified Dipolar Couplings for a PDB Structure Using Known Order Matrix Parameters

This server calculates dipolar couplings for an existing structure when given order matrix tensor parameters determined from a previous fit. The couplings to calculate are specified in the form of a DC input table.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/saupe.html

Calculate Specified Dipolar Couplings for a PDB Structure Using Known Alignment Tensor Parameters

This server calculates dipolar couplings for an existing structure when given a complete set of tensor parameters in terms of Magnitude, Rhombicity, and rotational angles. The couplings to calculate are specified in the form of a DC input table.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/fixed.html

Calculate General Classes of Dipolar Couplings for a PDB Structure (Proteins Only)

This server calculates dipolar couplings for an existing protein structure when given a complete set of tensor parameters in terms of Magnitude, Rhombicity, and rotational angles. The couplings to calculate are selected from one or more classes, such as HN-N, HA-CA, etc.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/general.html

Generate a PDB File with Atom Pairs in Random Orientations

This server creates a PDB file containing only HN-N atom pairs in random orientations, for the purpose of performing hypothesis testing of dipolar coupling analysis. It also creates a corresponding table of synthetic dipolar couplings.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/rand.html

Dipolar Coupling Tensor Analysis by Molecular Fragment Replacement (MFR)

(Protein Data Only) This server performs a dipolar coupling protein fragment homology search. In addition to providing structural information and identifying possible structural homologs, this search can also be used to characterize the alignment tensor before the target structure is known.

Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/mfr.html

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last update: Mar 25 2012