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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
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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
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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
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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
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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
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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
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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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Orthogonalize Dipolar Coupling Tensors using SVD and Generate Orthogonalized RDC Datasets
This server performs orthogonalization for a set of dipolar coupling alignment tensors obtained from multiple alignment media
and generate sets of residual dipolar couplings that correspond to orthogonal alignment tensors.
Server: http://spin.niddk.nih.gov/bax/nmrserver/dc/orth.html
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