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PDBsum entry 1ccn
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Plant seed protein
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PDB id
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1ccn
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Contents |
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* Residue conservation analysis
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J Biomol Nmr
1:305-309
(1991)
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PubMed id:
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Direct NOE refinement of biomolecular structures using 2D NMR data.
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A.M.Bonvin,
R.Boelens,
R.Kaptein.
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ABSTRACT
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A set of computer programs called DINOSAUR has been developed, which allows the
refinement of biomolecular structures directly from 2D NOE intensities. The NOE
restraining potential implemented emphasises the weak intensities corresponding
to larger distances which are more likely to determine the three-dimensional
structure. An approximation based on a two-spin approximation is proposed for
the gradient of the NOE intensities instead of the exact solution which is
extremely time-consuming. The DINOSAUR routines have been implemented in various
refinement programs (Distance bound Driven Dynamics, Molecular Dynamics and
Energy Minimisation) and tested on an eight-residue model peptide.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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W.Gronwald,
K.Brunner,
R.Kirchhöfer,
J.Trenner,
K.P.Neidig,
and
H.R.Kalbitzer
(2007).
AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.
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J Biomol NMR,
37,
15-30.
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J.Malicka,
M.Groth,
C.Czaplewski,
W.Wiczk,
and
A.Liwo
(2002).
Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3.
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Biopolymers,
63,
217-231.
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M.Groth,
J.Malicka,
S.Rodziewicz- Motowidło,
C.Czaplewski,
L.Klaudel,
W.Wiczk,
and
A.Liwo
(2001).
Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models.
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Biopolymers,
60,
79-95.
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A.M.Bonvin,
J.A.Rullmann,
R.M.Lamerichs,
R.Boelens,
and
R.Kaptein
(1993).
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
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Proteins,
15,
385-400.
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PDB code:
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A.T.Brünger,
and
M.Nilges
(1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
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Q Rev Biophys,
26,
49.
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R.Nibedita,
R.A.Kumar,
A.Majumdar,
and
R.V.Hosur
(1992).
Simulation of NOESY spectra of DNA segments: a new scaling procedure for iterative comparison of calculated and experimental NOE intensities.
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J Biomol NMR,
2,
467-476.
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R.Nibedita,
R.A.Kumar,
A.Majumdar,
and
R.V.Hosur
(1992).
Quantitative comparison of experimental and simulated NOE intensities: correlation with accuracy of oligonucleotide structure determination.
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J Biomol NMR,
2,
477-484.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
