Example Xplor-NIH input scripts and associated files
All examples make use of the IVM (internal variable module):
Schwieters, C.D. & Clore, G.M. (2001) Internal coordinates
for molecular dynamics and minimization in structure determination
and refinement. J. Magn. Reson. 152, 288-302. pubmed
PDF
Documentation of python interface
General script for protein structure refinement: includes 1H-chemical shifts, backbone and side chain dipolar couplings, 13C alpha/beta chemical shifts, J couplings, radius of gyration, torsion angle database potential of mean force, etc.... This script can also be used with minor modification to fold structures from an extended strand or random coil (use asymptotic NOE potential instead of regular square-well).
Refinement of B1 domain of protein G: includes dipolar couplings in 2 media, J couplings, radius of gyration and torsion angle database potential. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1999) Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J. Am. Chem. Soc. 121, 2337-2338. PDF
Docking of protein-protein
complexes based on highly ambiguous distance restraints derived
from chemical shift mapping and dipolar couplings
Clore, G.M. & Schwieters, C.D. (2003) Docking of protein-protein
complexes on the basis of highly ambiguous intermolecular distance
restraints derived from 1HN/15N
chemical shift mapping and backbone 15N-1H
residual dipolar couplings using conjoined rigid body/torsion
angle dynamics. J. Am. Chem. Soc. 125, 2902-2912. Pubmed
PDF
Refinement of a protein-ssDNA
complex (includes dipolar couplings, database potentials, etc..)
Braddock, D.T., Louis, J.M., Baber, J.L., Levens, D. &
Clore, G.M. (2002) Structure and dynamics of KH domains from FBP
bound to single stranded DNA. Nature 415, 1051-1056. pubmed
PDF
Braddock, D.T., Baber, J.L., Levens, D. & Clore, G.M. (2002)
Molecular basis of sequence specific single-stranded DNA recognition
by KH domains: solution structure of a complex between hnRNP K
KH3 and single-stranded DNA. EMBO J. 21, 3476-3485. Pubmed
PDF
DNA refinement using base-base
and torsion angle database potentials (includes dipolar couplings
and 31P-CSA)
Kuszewski, J., Schwieters, C.D. & Clore, G.M. (2001)
Improving the accuracy of NMR structures of DNA by means of a
database potential of mean force describing base-base positional
interactions. J. Am. Chem. Soc. 123, 3903-3918. pubmed
PDF
RNA refinement using base-base
and torsion angle database potentials (includes dipolar couplings)
Clore, G.M. & Kuszewski, J. (2003) Improving the accuracy
of NMR structures of RNA by means of conformational database potentials
of mean force as assessed by complete dipolar coupling cross-validation.
J. Am. Chem. Soc. 125, 1518-1525. Pubmed
PDF
Ensemble refinement of dipolar couplings
recorded in multiple alignment media and analysis of amplitudes
of backbone dynamics and correlated motions.
Clore, G.M. & Schwieters, C.D. (2004) How much backbone motion
in ubiquitin is required to be consistent with dipolar coupling
data measured in multiple alignment media as assessed by independent
cross-validation. J. Am. Chem. Soc. 126, 2923-2938. Pubmed
PDF Supplementary
Information
Clore, G.M. & Schwieters, C. D. (2004) Amplitudes
of protein backbone dynamics and correlated motions in a small
a/b protein:
correspondence of dipolar coupling and heteronuclear relaxation
measurements. Biochemistry 43, 10678-10691. Pubmed
PDF Supplementary
Information
Ensemble refinement for PRE
data.
Iwahara, J., Schwieters, C. D., Clore, G. M. (2004) Ensemble approach
for NMR structure refinement against 1H paramagnetic
relaxation enhancement data arising from a flexible paramagnetic
group attached to a macromolecule. J. Am. Chem. Soc. 126,
5879-5896. Pubmed
PDF Supplementary
Information
Completely automated NMR structure
determination using the PASD algorithm
Kuszewski, J., Schwieters, C.D., Garrett, D.S., Byrd, R.A., Tjandra,
N. & Clore, G. M. (2004) Completely automated, highly error
tolerant macromolecular structure determination from multidimensional
nuclear Overhauser enhancement spectra and chemical shift assignments.
J. Am. Chem. Soc. 126, 6258-6273. Pubmed
PDF
Rigid body docking
using sparse NOE restraints and a reduced radius of gyration restraint
Tang,C. & Clore, G.M. (2006) A simple and reliable approach
to docking protein-protein complexes from very sparse NOE-derived
intermolecular distance restraints. J. Biomol. NMR 36,
37-44.
Pubmed PDF
Ensemble refinement against
RDCs, relaxation order parameters and crystallographic B-factors
Clore, G.M. & Schwieters, C.D. (2006) Concordance of residual
dipolar couplings, backbone order parameters and crystallographic
B-factors for a small a/b
protein: a unified picture of high probability, fast atomic motions
in proteins. J. Mol. Biol. 355, 879-886. Pubmed
PDF Coordinates
for N=8 ensemble
Ensemble refinement of DNA
against RDCs and Large Angle X-ray scattering data.
Schwieters, C.D. & Clore, G.M. (2007) A physical picture
of atomic motions within the Dickerson DNA dodecamer in solution
derived from joint ensemble refinement against NMR and large angle
X-ray scattering data. Biochemistry 46, 1152-1166. Pubmed
PDF Supplementary
Material Coordinates
for N=4 ensemble
Miscellaneous useful python scripts in Xplor-NIH
Python script for automatic generation of psf file from sequence (protein or nucleic acid)