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)

Python script for generation of torsion angles and torsion angle statistics for an ensemble of structures

 

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