Summary
A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of ‘strips’, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.
Similar content being viewed by others
Abbreviations
- 1D, 2D, 3D, 4D:
-
one-, two-, three-, four-dimensional
- NOE:
-
nuclear Overhauser enhancement
- NOESY:
-
nuclear Overhauser enhancement spectroscopy
- TOCSY:
-
total correlation spectroscopy
- COSY:
-
correlation spectroscopy
- TPPI:
-
time-proportional phase incrementation
References
BartelsC. and WüthrichK. (1994) J. Biomol. NMR, 4, 775–785.
BaxA., CloreG.M. and GronenbornA.M. (1990) J. Magn. Reson., 88, 425–431.
BaxA. and GrzesiekS. (1993) Acc. Chem. Res., 26, 131–138.
BernsteinR., CieslarC., RossA., OschkinatH., FreundJ. and HolakT.A. (1993) J. Biomol. NMR, 3, 245–251.
BilleterM., BasusV.J. and KuntzI.D. (1988) J. Magn. Reson., 76, 400–415.
BushwellerJ., BilleterM., HolmgrenA. and WüthrichK. (1994) J. Mol. Biol., 235, 1585–1597.
CieslarC., CloreG.M. and GronenbornA.M. (1988) J. Magn. Reson, 80, 119–127.
DriscollP.C., CloreG.M., MarionD., WingfieldP.T. and GronenbornA.M. (1990) Biochemistry, 29, 3542–3556.
EadsC.D. and KuntzI.D. (1989) J. Magn. Reson., 82, 467–482.
EcclesC., GüntertP., BilleterM. and WüthrichK. (1991) J. Biomol. NMR, 1, 111–130.
FesikS.W. and ZuiderwegE.R.P. (1988) J. Magn. Reson., 78, 588–593.
GarretD.S., PowersR., GronenbornA.M. and CloreG.M. (1991) J. Magn. Reson., 95, 214–220.
GlaserS. and KalbitzerH.R. (1987) J. Magn. Reson., 74, 450–463.
GrahnH., DelaglioF., DelsueM.A. and LevyG.C. (1988) J. Magn. Reson., 77, 294–307.
GrayB.N. and BrownL.R. (1991) J. Magn. Reson., 95, 320–340.
GrossK.-H. and KalbitzerH.R. (1988) J. Magn. Reson., 76, 87–99.
GrzesiekS. and BaxA. (1992a) J. Am. Chem. Soc., 114, 6291–6293.
GrzesiekS. and BaxA. (1992b) J. Magn. Reson, 99, 201–207.
GüntertP., QianY.Q., OttingG., MüllerM., GehringW. and WüthrichK. (1991) J. Mol. Biol., 217, 531–540.
GüntertP., DötschV., WiderG. and WüthrichK. (1992) J. Biomol. NMR, 2, 619–629.
GüntertP., BerndtK.D. and WüthrichK. (1993) J. Biomol. NMR, 3, 601–606.
HareB.J. and PrestegardJ.H. (1994) J. Biomol. NMR, 4, 35–46.
HellerD. (1991) Motif Programming Manual, O'Reilly & Associates, Inc., Sebastopol, CA.
HochJ.C., HengyiS., KjærM., LudvigsenS. and PoulsenF.M. (1987) Carlsberg Res. Commun., 52, 111–122.
IkuraM., KayL.E., TschudinR. and BaxA. (1989) J. Magn. Reson., 86, 204–209.
IkuraM., KayL.E. and BaxA. (1990) Biochemistry, 29, 4659–4667.
JungnickelD. (1990) Graphen, Netzwerke und Algorithmen, Bibliographisches Institut Wissenschaftsverlag, Mannheim.
KleywegtG.J., LamerichsR.M.J.N., BoelensR. and KapteinR. (1989) J. Magn. Reson., 85, 186–197.
KleywegtG.J., BoelensR., CoxM., LlinásM. and KapteinR. (1991) J. Biomol. NMR, 1, 111–130.
KleywegtG.J., VuisterG.W., PadillaA., KnegtelR.M.A., BoelensR. and KapteinR. (1993) J. Magn. Reson. Ser. B. 102, 166–176.
KraulisP.J. (1989) J. Magn. Reson., 84, 627–633.
MeadowsR.P., OlejniczakE.T. and FesikS.W. (1994) J. Biomol. NMR, 4, 79–96.
NeidigK.P., BodenmüllerH. and KalbitzerH.R. (1984) Biochem. Biophys. Res. Commun., 125, 1143–1150.
NovicM., OschkinatH., PfändlerP. and BodenhausenG. (1987) J. Magn. Reson., 73, 493–511.
O'ConnellJ.F., BenderR., EngelsJ.W., KollerK.P., ScharfM. and WüthrichK. (1994) Eur. J. Biochem., 220, 763–770.
PfändlerP., BodenhausenG., MeierB.U. and ErnstR.R. (1985) Anal. Chem., 57, 2510–2516.
PfändlerP. and BodenhausenG. (1990) J. Magn. Reson., 87, 26–45.
RicharzR. and WüthrichK. (1978) Biopolymers, 17, 2133–2141.
ScheiferR.W., GettysJ. and NewmanR. (1988) X Window System C Library and Protocol Reference, Digital Press, Bedford, MA.
SimorreJ.P., BrutscherB., CaffreyM.S. and MarionD. (1994) J. Biomol. NMR, 4, 325–333.
SpitzfadenC., BraunW., WiderG., WidmerH. and WüthrichK. (1994) J. Biomol. NMR, 4, 463–482.
StatesD.J., HaberkornR.A. and RubenD.J. (1982) J. Magn. Reson., 48, 286–292.
StovenV., MikouA., PiveteauD., GuittetE. and LallemandJ.Y. (1989) J. Magn. Reson. 82, 163–168.
SzyperskiT., WiderG., BushwellerJ.H. and WüthrichK. (1993a) J. Biomol. NMR, 3, 127–132.
SzyperskiT., WiderG., BushwellerJ.H. and WüthrichK. (1993b) J. Am. Chem. Soc., 115, 9307–9308.
SzyperskiT., PellecchiaM. and WüthrichK. (1994a) J. Magn. Reson. Ser. B, 105, 188–191.
SzyperskiT., PellecchiaM., WallD., GeorgopoulosC. and WüthrichK. (1994b) Proc. Natl. Acad. Sci. USA, 91, 11343–11347.
Van deVenF.J.M. (1990) J. Magn. Reson., 86, 633–644.
WeberP.L., MalikayilJ.A. and MüllerL. (1989) J. Magn. Reson., 82, 419–426.
WehrensR., LucasiusC., BuydensL. and KatemanG. (1993) J. Chem. Inf. Comput. Sci., 33, 245–251.
WüthrichK., BilleterM. and BraunW. (1983) J. Mol. Biol., 169, 949–961.
WüthrichK. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.
WüthrichK., SpitzfadenC., MemmertK., WidmerH. and WiderG. (1991) FEBS Lett., 285, 237–247.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Bartels, C., Xia, Th., Billeter, M. et al. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6, 1–10 (1995). https://doi.org/10.1007/BF00417486
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00417486