Using Xplor-NIH for NMR molecular structure determination

Progress in Nuclear Magnetic Resonance Spectroscopy

Volumn 48, Issue 1, 2006, Pages 47-62

  Schwieters, Charles D ^a   Kuszewski, John J ^a   Marius Clore, G ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Computational Toolbox; NMR restraints; Nucleic acids; Optimization; Proteins; Structure determination

Indexed keywords

COMPUTER SIMULATION; DATABASE SYSTEMS; KNOWLEDGE BASED SYSTEMS; MOLECULAR DYNAMICS; MONTE CARLO METHODS; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACIDS; OBJECT ORIENTED PROGRAMMING; PROTEINS; STRUCTURE (COMPOSITION); TORSIONAL STRESS;

COMPUTATIONAL TOOLBOX; NMR RESTRAINTS; STRUCTURE DETERMINATION; XPLOR-NIH [1];

MOLECULAR STRUCTURE;

EID: 33645868288     PISSN: 00796565     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pnmrs.2005.10.001     Document Type: Review

References (80)

1. Schwieters C.D., Kuszewski J.J., Tjandra N., and Clore G.M. J. Magn. Reson. 160 (2003) 66-74
2. Brünger A.T. XPLOR Manual Version 3.1 (1993), Yale University Press, New Haven 1355. http://xplor.csb.yale.edu/xplor-info/ Available online at
3. Kuszewski J., Gronenborn A.M., and Clore G.M. J. Am. Chem. Soc. 121 (1999) 2337-2338
4. Tjandra N., Marquardt J., and Clore G.M. J. Magn. Reson. 142 (2000) 393-396
5. Cornilescu G., and Bax A. J. Am. Chem. Soc. 122 (2000) 10143-10154
6. Banci L., Bertini I., Cavallaro G., Giachetti A., Luchinat C., and Parigi G. J. Biomol. NMR 28 (2004) 249-261
7. Iwahara J., Schwieters C.D., and Clore G.M. J. Am. Chem. Soc. 126 (2004) 5879-5896
8. Kuszewski J., and Clore G.M. J. Magn. Reson. 146 (2000) 249-254
9. Kuszewski J., Schwieters C.D., and Clore G.M. J. Am. Chem. Soc. 123 (2001) 3903-3918
10. Clore G.M., and Kuszewski J. J. Am. Chem. Soc. 124 (2002) 2866-2867
11. Schwieters C.D., and Clore G.M. J. Magn. Reson. 152 (2001) 288-302
12. Kuszewski J., Schwieters C.D., Garrett D.S., Byrd R.A., Tjandra N., and Clore G.M. J. Am. Chem. Soc. 126 (2004) 6258-6273
13. Clore G.M., and Schwieters C.D. J. Am. Chem. Soc. 126 (2004) 2923-2938
14. Clore G.M., and Schwieters C.D. Biochemistry 43 (2004) 10678-10691
15. Schwieters C.D., and Clore G.M. J. Magn. Reson. 149 (2001) 239-244
16. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G. Acta Crystallogr. Ser. D 54 (1998) 905-921
17. Available online at: http://www.swig.org/
18. Lutz M., and Ascher D. Learning Python. second ed. (2004), O'Reilly, Sebastopol, CA. http://python.org Available online at
19. Available online at: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/index.html
20. Kuszewski J., Gronenborn A.M., and Clore G.M. Protein Sci. 5 (1996) 1067-1080
21. Kuszewski J., Gronenborn A.M., and Clore G.M. J. Magn. Reson. 125 (1997) 171-177
22. Brünger A.T., Kuriyan J., and Karplus M. Science 235 (1987) 458-460
23. Brünger A.T. In: Isaacs N.W., and Taylor M.R. (Eds). Crystallographic Computing 4: Techniques and New Technologies (1988), Clarendon Press, Oxford 126-140
24. Brünger A.T. Nature 355 (1992) 472-475
25. Shaanan B., Gronenborn A.M., Cohen G.H., Gilliland G.L., Veerapandian B., Davies D.R., and Clore G.M. Science 257 (1992) 961-964
26. Nilges M., Gronenborn A.M., Brünger A.T., and Clore G.M. Protein Eng. 2 (1988) 27-38
27. Nilges M. Proteins 17 (1993) 297-309
28. Wüthrich K., Billeter M., and Braun W. J. Mol. Biol. 169 (1983) 949-961
29. Bax A., Kontaxis G., and Tjandra N. Methods Enzymol. 339 (2001) 127-174
30. Tjandra N., Omichinski J.G., Gronenborn A.M., Clore G.M., and Bax A. Nat. Struct. Biol. 4 (1997) 732-738
31. Clore G.M., Gronenborn A.M., and Tjandra N. J. Magn. Reson. 131 (1998) 159-162
32. Wu Z., Tjandra N., and Bax A. J. Am. Chem. Soc. 123 (2001) 3617-3618
33. Lipsitz R.S., and Tjandra N. J. Am. Chem. Soc. 123 (2001) 11065-11066
34. Ottiger M., and Bax A. J. Am. Chem. Soc. 119 (1997) 8070-8075
35. Garrett D.S., Kuszewski J., Hancock T.J., Lodi P.J., Vuister G.W., Gronenborn A.M., and Clore G.M. J. Magn. Reson. Ser. B 104 (1994) 99-103
36. Engh R.A., and Huber R. Acta Crystallogr. A 47 (1991) 392-400
37. Braun W., and Go N. J. Mol. Biol. 186 (1985) 611-626
38. Némethy G., Pottle M.S., and Scheraga H.A. J. Phys. Chem. 87 (1983) 1883-1887
39. Jorgensen W.L., and Tirado-Rives J. J. Am. Chem. Soc. 110 (1988) 1666-1671
40. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., and Weiner P. J. Am. Chem. Soc. 106 (1984) 765-784
41. Schuettelkopf A.W., and van Aalten D.M.F. Acta Crystallogr D60 (2004) 1355-1363. http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Available online at:
42. Kleywegt G.J., Zou J.Y., Kjeldgaard M., and Jones T.A. In: Rossmann M.G., and Arnold E. (Eds). International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules (2001), Kluwer Academic Publishers, Dordrecht 353-356. http://xray.bmc.uu.se/gerard/manuals/xplo2d_man.html (see also pp. 366-367) Available online at
43. Nilges M., Clore G.M., and Gronenborn A.M. FEBS Lett. 229 (1988) 317-324
44. Linge J.P., and Nilges M. J. Biomol. NMR 13 (1999) 51-59
45. Linge J.P., Williams M.A., Spronk C.A.E.M., Bonvin A.M.J.J., and Nilges M. Proteins 50 (2003) 496-506
46. Nabuurs S.B., Nederveen A.J., Vranken W., Doreleijers J.F., Bonvin A.M.J.J., Vuister G.W., Vriend G., and Spronk C.A.E.M. Proteins 55 (2004) 483-486
47. Simonson T. Curr. Opin. Struct. Biol. 11 (2001) 243
48. Skolnick J., Kolinski A., and Ortiz A.R. J. Mol. Biol. 265 (1997) 217-241
49. Clore G.M., Nilges M., Sukumaran D.K., Brünger A.T., Karplus M., and Gronenborn A.M. EMBO J. 5 (1986) 2729-2735
50. J. Kuszewski, G.M. Clore, unpublished.
51. Vuister G.W., Delaglio F., and Bax A. J. Biomol. NMR 3 (1993) 67-80
52. Kuszewski J., Qin J., Gronenborn A.M., and Clore G.M. J. Magn. Reson. Ser. B 106 (1995) 92-96
53. Spera S., and Bax A. J. Am. Chem. Soc. 113 (1991) 5490-5492
54. Kuszewski J., Gronenborn A.M., and Clore G.M. J. Magn. Reson. Ser. B 107 (1995) 293-297
55. Kuszewski J., Gronenborn A.M., and Clore G.M. J. Magn. Reson. Ser. B 112 (1996) 79-81
56. Yip P., and Case D.A. J. Magn. Reson. 83 (1989) 643-648
57. Nilges M., Habazettl J., Brünger A.T., and Holak T.A. J. Mol. Biol. 219 (1991) 499-510
58. Tjandra N., Garrett D.S., Gronenborn A.M., Bax A., and Clore G.M. Nat. Struct. Biol. 4 (1997) 443-449
59. Clore G.M., Gronenborn A.M., Szabo A., and Tjandra N. J. Am. Chem. Soc. 120 (1998) 4889-4890
60. Sass H.J., Musco G., Stahl S.J., Wingfield P.T., and Grzesiek S. J. Biomol. NMR 21 (2001) 275-280
61. Meiler J., Blomberg N., Nilges M., and Griesinger C. J. Biomol. NMR 16 (2000) 245-252
62. Lipsitz R.S., Sharma Y., Brooks B.R., and Tjandra N. J. Am. Chem. Soc. 124 (2002) 10621-10626
63. Grishaev A., and Bax A. J. Am. Chem. Soc. 126 (2004) 7281-7292
64. Clore G.M., and Kuszewski J. J. Am. Chem. Soc. 125 (2003) 1518-1525
65. J. Kuszewski, G.M. Clore, unpublished.
66. Zuo X., and Tiede D.M. J. Am. Chem. Soc. 127 (2005) 16-17
67. Bae D.-S., and Haug E.J. Mech. Struct. Mach. 15 (1987) 359
68. Rodriguez G., Jain A., and Kreutz-Delgado K. J. Austron. Sci. 40 (1992) 27
69. Jain A., Vaidehi N., and Rodriguez G. J. Comput. Phys. 106 (1993) 258
70. Clore G.M., and Gronenborn A.M. CRC Crit. Rev. Biochem. Mol. Biol. 24 (1989) 479-564
71. Palmer III A.G. Annu. Rev. Biophys. Biomol. Struct. 30 (2001) 129-155
72. Pearlman D.A., and Kollman P.A. J. Mol. Biol. 220 (1991) 457-479
73. Lipari G., and Szabo A. J. Am. Chem. Soc. 104 (1982) 4559-4570
74. G.M. Clore, C.D. Schwieters, J. Mol. Biol. in press.
75. Humphrey W., Dalke A., and Schulten K. J. Mol. Graphics 14 (1996) 33-38. http://www.ks.uiuc.edu/Research/vmd/ Available online at
76. Brünger A.T., Clore G.M., Gronenborn A.M., Saffrich R., and Nilges M. Science 261 (1993) 328-331
77. Clore G.M., and Garrett D.S. J. Am. Chem. Soc. 121 (1999) 9008-9012
78. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. J. Appl. Crystallogr 26 (1993) 283-291. http://www.biochem.ucl.ac.uk/roman/procheck/procheck.html Available online at
79. Hooft R.W.W., Vriend G., Sander C., and Abola E.E. Nature 381 (1996) 272. http://swift.cmbi.kun.nl/whatif/ Available online at
80. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. J. Comput. Chem. 4 (1983) 187-217