Xplor-NIH references Xplor-NIH Schwieters, C.D., Kuszewski, J.J., Tjandra, N. & Clore, G.M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 66-74. New Refinement tools 1. Garrett, D.S., Kuszewski, J., Hancock, T.J., Lodi, P.J., Vuister, G.W., Gronenborn, A.M. & Clore, G.M. (1994) The impact of direct refinement against three-bond HN-C_H coupling constants on protein structure determination by NMR. J. Magn. Reson. Series B 104, 99-103. 2. Kuszewski, J., Qin, J., Gronenborn, A.M. & Clore, G.M. (1995) The impact of direct refinement against 13C_alpha and 13C_beta chemical shifts on protein structure determination by NMR. J. Magn. Reson Series B 106, 92-96. 3. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1995) The impact of direct refinement against proton chemical shifts in protein structure determination by NMR. J. Magn. Reson. Series B 107, 293-297 4. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1996) A potential involving multiple proton chemical shift restraints for non-stereospecifically assigned methyl and methylene protons. J. Magn. Reson. Series B 112, 79-81. 5. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1996) Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Science 5, 1067-1080. 6. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1997) Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125, 171-177. 7. Tjandra, N., Garrett, D.S., Gronenborn, A.M., Bax, A. & Clore, G.M. (1997) Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nature Struct. Biol.4, 443-449. 8. Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. & Bax, A. (1997) Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct. Biol. 4, 732-738. 9. Clore, G.M. & Gronenborn, A. M. (1998) New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. U.S.A. 95, 5891-5898. 10. Clore, G.M., Gronenborn, A.M. & Tjandra, N. (1998) Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131, 159-162. 11. Clore, G.M., Gronenborn, A.M. & Bax, A. (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson. 133, 216-221. 12. Clore, G.M., Gronenborn, A.M., Szabo, A. & Tjandra, N. (1998) Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information. J. Am. Chem. Soc. 120, 4889-4890. 13. 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. 15. Clore, G.M., Starich, M.R., Bewley, C.A., Cai, M. & Kuszewski, J. (1999) Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints. J. Am. Chem. Soc. 121, 6513-6514. 16. Tjandra, N., J. Marquardt, J. & Clore, G.M. (2000) Direct refinement against proton-proton dipolar couplings in NMR structure determination of macromolecules. J. Magn. Reson. 142, 393-396. 17. Clore, G.M. (2000) Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization. Proc. Natl. Acad. Sci. U.S.A. 97, 9021-9025. 18. Bewley, C.A. & Clore, G.M. (2000) Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization. J. Am. Chem. Soc. 122, 6009-6016. 19. Kuszewski, J. & Clore, G.M. (2000) Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force. J. Magn. Reson. 146, 249-254. 20. 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. 21. 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. 22. Donaldson, L. W.; Skrynnikov, N. R.; Choy, W.-Y.; Muhandiram, D. R.; Sarkar, B.; Forman-Kay, J. D.; Kay, L. E., Structural Characterization of Proteins with an Attached ATCUN Motif by Paramagnetic Relaxation Enhancement NMR Spectroscopy, J. Am. Chem. Soc. 123, 9843-9847 (2001). 23. Clore, G.M. & Bewley, C.A. (2002) Using conjoined rigid body / torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings. J. Magn. Reson. 154, 329-335. 24. Clore, G.M. & Kuszewski, J. (2002) chi1 rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force. J. Am. Chem. Soc. 124, 2866-2867 25. Wu, Z., Tjandra, N. & Bax A. (2001) 31P chemical shift anisotropy as an aid in determining nucleic acid structure in liquid crystals. J. Am. Chem. Soc. 123, 3617-3618. 26. Lipsitz, R.S. & Tjandra, N. (2001) Carbonyl CSA restraints from solution NMR for protein structure refinement. J. Am. Chem. Soc. 123, 11065-11066. 27. Lipsitz, R.S., Sharma, Y., Brooks, B.R. & Tjandra, N. (2002) Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. J Am Chem Soc. 124, 10621-10626. 28. 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. 29. 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. 30. L. Banci, I. Bertini, G. Cavallaro, A. Giachetti, C. Luchinat, G. Parigi Paramagnetism-based restraints for Xplor-NIH. Journal of Biomolecular NMR 28, 249-261 (2004); http://www.postgenomicnmr.net/SW/PARArestraints.html. 31. H.J. Sass, G. Musco, S.J. Stahl, P.T. Wingfield and S.Grzesiek, "An easy way to include weak alignment constaints into NMR structure calculations", J. Biomol. NMR 21: 275-280 (2001). 32. A. Grishaev and A. Bax. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J. Am. Chem. Soc. 126, 7281-7292 (2004). 33. A. Grishaev, J. Ying, A. Bax "Pseudo-CSA restraints for NMR refinement of nucleic acid structure," J. Am. Chem. Soc. 128, 10010-10011 (2006). 34. G.M. Clore and C.D. Schwieters "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 (2004). 35. Chenqi Xu, Etienne Gagnon, Matthew E. Call, Jason R. Schnell, Charles D. Schwieters, Christopher V. Carman, James J. Chou, and Kai W. Wucherpfennig, ``Regulation of T cell Receptor Activation by Dynamic Membrane Binding of the CD3epsilon Cytoplasmic Tyrosine-Based Motif,'' Cell 135, 702-713 (2008). 36. Y. Tian, C.D. Schwieters, S.J. Opella, and F.M. Marassi, ``A Practical Implicit Solvent Potential for NMR Structure Calculation,'' J. Magn. Res. 243, 54-64 (2014). VMD-XPLOR Graphics package 1. Schwieters, C.D. & Clore, G.M. (2001) The VMD-XPLOR visualization package for NMR structure refinement. J. Magn. reson.149, 239-244. 2. Schwieters, C.D. & Clore, G.M. (2002) Reweighted atomic densities to represent ensembles of NMR structures. J. Biomol. NMR 23, 221-225. Marvin/PASD J. Kuszewski, C.D. Schwieters, D.S. Garrett, R.A. Byrd, N. Tjandra and G.M. Clore. ``Completely automated, highly error tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignment,'' J. Am. Chem. Soc. 126, 6258-6273 (2004). J.J. Kuszewski, R. Augustine Thottungal, G.M. Clore, and C.D. Schwieters, ``Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm,'' J. Biomol. NMR 41, 221-239 (2008). CNS 1. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunsteleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. & Warren, G.L. (1998) Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Cryst. Series D 54, 901-921. Cross-validation 1. Brünger, A.T., Clore, G.M., Gronenborn, A.M., Saffrich, R. & Nilges, M. (1993) Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261, 328-331 2. Clore, G.M. & Garrett, D.S. (1999) R-factor, Free R and complete cross-validation for dipolar coupling refinement of NMR structures. J. Am. Chem. Soc. 121, 9008-9012. Simulated annealing 1. Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988) Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett 229, 317-324 2. Nilges, M., Gronenborn, A.M., Brünger, A.T. & Clore, G.M. (1988) Determination of three- dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Engineering 2, 27-38 3. Nilges, M., Clore, G.M. & Gronenborn, A.M. (1988) Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Letters 239, 129-136 7. Clore, G.M. & Gronenborn, A.M. (1989) Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. CRC Critical Reviews in Biochemistry and Molecular Biology 24, 479-564 Joint NMR/X-ray refinement 1. Shaanan, B., Gronenborn, A.M., Cohen, G.H., Gilliland, G.L., Veerapandian, B., Davies, D.R. & Clore, G.M. (1992) Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science 257, 961-964 Some General references 1. Clore, G.M., Gronenborn, A.M., Brunger, A.T. & Karplus, M. (1985) The solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli: combined use of 1H-nuclear magnetic resonance and restrained molecular dynamics. J. Mol. Biol. 186, 435-455. 2. Nilsson, L., Clore, G.M., Gronenborn, A.M., Brunger, A.T. & Karplus, M. (1986) Structure refinement of oligonucleotides by molecular dynamics with NOE interproton distance restraints: application to 5'd(CGTACG)2. J. Mol. Biol. 188, 455-475. 3. Brunger, A.T., Clore, G.M., Gronenborn, A.M. & Karplus, M. (1986) Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. U.S.A. 83, 3801-3805. 4. Clore, G.M., Brunger, A.T., Karplus, M. & Gronenborn, A.M. (1986) Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: a model study of crambin. J. Mol. Biol. 191, 523-551. 5. Clore, G.M., Nilges, M., Sukumaran, D.K., Brunger, A.T., Karplus, M. & Gronenborn, A.M. (1986) The three-dimensional structure of a1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 5, 2729- 2735. 6. Gronenborn, A.M. & Clore, G.M. (1995) Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. CRC Crit. Rev. Biochem. Mol. Biol. 30, 351- 385 7. Clore, G.M. & Gronenborn, A.M. (1998) Determining structures of large proteins and protein complexes by NMR. Trends in Biotechnology 16, 22-34 8. Clore, G.M. & Schwieters, C.D. (2002) Theoretical and computational advances in biomolecular NMR spectroscopy. Curr. Op. Struct. Biol. 12, 146-153. Generalized Born 1. Wagner, F. & Simonson, T., Implicit solvent models: combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. J Comp Chem (1999) 20, 322-335. 2. Still, W.C., Tempxzyk, A., Hawley, R., and Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990), 6127-6129. 3. Hawkins, G. Cramer, C., and Truhlar, D. Pairwise descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246 (1995), 122-129. 4. Schaefer, M. & Karplus, M. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 100 (1996), 1578-1599. 5. Qiu D, Shenkin PS, Hollinger FP, Still WC, The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A 101, 3005-3014 (1997). 6. T Simonson, Curr Opin Struc Biol 11, 243 (2001). FX-PLOR: Refinement against Fiber Diffraction data 1. Wang, H., and Stubbs, G. (1993). ``Molecular dynamics in refinement against fiber diffraction data, Acta Cryst A49, 504--513. 2. Denny, R.C., Shotton, M.W., and Forsyth, V.T. (1997). ``X-PLOR for Polycrystalline Fibre Diffraction", Fibre Diffr. Rev. 6, 30-33.