Bibliography
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E., & Wüthrich, K. (1998). Recommendations for the presentation of NMR structures of proteins and nucleic acids â IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. Journal of Biomolecular NMR, 12(1), 1â23.
References
63
Referenced
331
-
Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A.R. and Schneider, B. (1992) The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids, Biophys. J., 63, 751–759. The Nucleic Acid Data Bank can be reached on the Internet at http://www.ndbserver.rutgers.edu:80/.
(
10.1016/S0006-3495(92)81649-1
) / Biophys. J. by H.M. Berman (1992) - Hendrickson, W.A. and Wüthrich, K. (1991) Macromolecular Structures, Current Biology, London, UK. / Macromolecular Structures by W.A. Hendrickson (1991)
- Nomenclature Committee of IUBMB (NC-IUBMB) and IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) (1992) Newsletter 1992, Biochem. Int., 26, 567–575; and references therein. / Biochem. Int. by Nomenclature Committee of IUBMB (1992)
- Commission on Molecular Structure and Spectroscopy (1972) Recommendations for Presentation of NMR Data for Publication in Chemical Journals,Pure Appl. Chem., 29, 627–628. / Pure Appl. Chem. by Commission on Molecular StructureSpectroscopy (1972)
- Commission on Molecular Structure and Spectroscopy (1976) Presentation of NMR Data for Publication in Chemical Journals-B. Conventions Relating to Spectra from Nuclei other than Protons (Recommendations 1975), Pure Appl. Chem., 45, 219. / Pure Appl. Chem. by Commission on Molecular StructureSpectroscopy (1976)
-
Harris, R.K., Kowalewski, J., and Cabral de Menezes, S. (1996) Parameters and Symbols for use in Nuclear Magnetic Resonance, draft IUPAC document to be published in Pure Appl. Chem., 69, 2489–2495.
(
10.1351/pac199769122489
) / Appl. Chem. by R.K. Harris (1996) - Liébecq, C. (Ed.) (1992) Biochemical Nomenclature and Related Documents - A Compendium, 2nd ed., Portland Press on behalf of IUBMB, London, U.K. / Biochemical Nomenclature and Related Documents - A Compendium (1992)
- Bonnett, R. (1978) In The Porphyrins (Ed., Dolphin, D.), Vol. 1, Part A, Academic Press, New York, NY, pp. 1–27. / The Porphyrins by R. Bonnett (1978)
- IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (1975) Nomenclature of Iron-Sulfur Proteins. Recommendations 1973, Eur. J. Biochem., 35, 1–2. / Eur. J. Biochem. by IUPAC-IUB Commission on Biochemical Nomenclature (1975)
-
IUPAC-IUB Commission on Biochemical Nomenclature (1975) The Nomenclature of Peptide Hormones, Recommendations 1974, Biochemistry, 14, 2559–2560; reprinted in the Compendium (ref. 9).
(
10.1021/bi00682a041
) / Biochemistry by IUPAC-IUB Commission on Biochemical Nomenclature (1975) -
IUPAC-IUB Commission on Biochemical Nomenclature (1972) Abbreviated Nomenclature of Synthetic Polypeptides (Polymerized Amino Acids), Revised Recommendations 1971, Biochemistry, 11, 942–944; reprinted in the Compendium (ref. 9).
(
10.1021/bi00755a039
) / Biochemistry by IUPAC-IUB Commission on Biochemical Nomenclature (1972) -
Nomenclature Committee of the International Union of Biochemistry (NC-IUB) Nomenclature for Incompletely Specified Bases in Nucleic Acids (1985), Eur. J. Biochem., 150, 1–5; reprinted in the Compendium (ref. 9).
(
10.1111/j.1432-1033.1985.tb08977.x
) / Eur. J. Biochem. by Nomenclature Committee of the International Union of Biochemistry (1985) - Protein Identification Resource, Georgetown University, Washington, D.C., U.S.A. The Protein Identification Resource can be searched with tools located at: http://www.gdb.org/Dan/proteins/pir.html.
- SWISS-PROT Annotated Protein Sequence Database (http://www.expasy.hcuge.ch/sprot/sprot-top.ht ml).
- International Union of Biochemistry and Molecular Biology (1992) Enzyme Nomenclature, Recommendations 1992, Academic Press, Orlando, FL, U.S.A. / Enzyme Nomenclature, Recommendations 1992 by International Union of BiochemistryMolecular Biology (1992)
- Chemical Abstracts Service, Columbus, OH, U.S.A. (http://info.cas.org/).
-
IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (1970) Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains, Tentative Rules 1969, Biochemistry, 9, 3471–3479; reprinted in the Compendium (ref. 9).
(
10.1021/bi00820a001
) / Biochemistry by IUPAC-IUB Commission on Biochemical Nomenclature (1970) -
IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1984) Nomenclature and Symbolism for Amino Acids and Peptides, Recommendations 1983, Eur. J. Biochem., 138, 9–37; reprinted in the Compendium (ref. 9).
(
10.1111/j.1432-1033.1984.tb07877.x
) / Eur. J. Biochem by IUPAC-IUB Joint Commission on Biochemical Nomenclature (1984) -
IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1983) Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains, Recommendations 1982, Eur. J. Biochem., 131, 9–15; reprinted in the Compendium (ref. 9).
(
10.1111/j.1432-1033.1983.tb07225.x
) / Eur. J. Biochem. by IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983) -
Hanson, K.R. (1966) Applications of the Sequence Rule. I. Naming the Paired Ligands g,g at a Tetrahedral Atom X
ggij. II. Naming the Two Faces of a Trigonal Atom Y
ghi, J. Am. Chem. Soc., 88, 2731–2742.
(
10.1021/ja00964a022
) / J. Am. Chem. Soc. by K.R. Hanson (1966) -
Cahn, R.S., Ingold, C.K. and Prelog, V. (1966) Specification of Molecular Chirality, Angew. Chem. Int. Ed. Engl., 5, 385–415; 511.
(
10.1002/anie.196603851
) / Angew. Chem. Int. Ed. Engl. by R.S. Cahn (1966) -
Prelog, V. and Helmchen, G. (1982) Basic Principles of the CIP-System and Proposals for a Revision, Angew. Chem. Int. Ed. Engl., 21, 567–583.
(
10.1002/anie.198205671
) / Angew. Chem. Int. Ed. Engl. by V. Prelog (1982) -
Blackwood, J.E., Gladys, C.L., Loening, K.L., Petrarca, A.E. and Rush, J.E. (1968) Unambiguous Specification of Stereoisomerism about a Double Bond, J. Am. Chem. Soc., 90, 509–510.
(
10.1021/ja01004a063
) / J. Am. Chem. Soc. by J.E. Blackwood (1968) -
Blackwood, J.E., Gladys, C.L., Petrarca, A.E., Powell, W.H. and Rush, J.E. (1968) Unique and Unambiguous Specification of Stereoisomerism about a Double Bond in Nomenclature and Other Notation Systems, J. Chem. Doc., 8, 30–32.
(
10.1021/c160028a007
) / J. Chem. Doc. by J.E. Blackwood (1968) -
IUPAC Commission on Nomenclature of Organic Chemistry (CNOC) (1976) Nomenclature of Organic Chemistry, Sec22 tion E: Stereochemistry, Recommendations 1974, Pure Appl. Chem., 45, 11–30 (1976); reprinted in the Compendium (ref. 9).
(
10.1351/pac197645010011
) / Pure Appl. Chem. by IUPAC Commission on Nomenclature of Organic Chemistry (1976) -
Wüthrich, K., Billeter, M. and Braun, W. (1983) Pseudo-Structures for the 20 Common Amino Acids for Use in Studies of Protein Conformations by Measurements of Intramolecular Proton-Proton Distance Constraints with Nuclear Magnetic Resonance, J. Mol. Biol., 169, 949–961.
(
10.1016/S0022-2836(83)80144-2
) / J. Mol. Biol. by K. Wüthrich (1983) - Koning, T.M.G., Boelens, R. and Kaptein, R. (1990) Calculation of the Nuclear Overhauser Effect and Determination of Proton-Proton Distances in the Presence of Internal Motions, J. Magn. Reson., 90, 111–123. / J. Magn. Reson. by T.M.G. Koning (1990)
- Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley Interscience, New York, NY. / NMR of Proteins and Nucleic Acids by K. Wüthrich (1986)
-
Güntert, P., Braun, W. and Wüthrich, K. (1991) Efficient Computation of Three-Dimensional Protein Structures in Solution from Nuclear Magnetic Resonance Data Using the Program DIANA and the Supporting Programs CALIBA, HABAS and GLOMSA, J. Mol. Biol., 217, 517–530.
(
10.1016/0022-2836(91)90754-T
) / J. Mol. Biol. by P. Güntert (1991) -
Historical changes in the definition of these angles have contributed to confusion. Their use in numerous textbooks does not conform to the current IUPAC-IUBMB nomenclature: Clauwaert, J. and Xia, J.-Z. (1993) Straightening out the Dihedral Angles, Trends Biochem. Sci., 18, 317–318; 464.
(
10.1016/0968-0004(93)90063-S
) / Trends Biochem. Sci. by J. Clauwaert (1993) -
Wilmott, C.M. and Thornton, J.M. (1990) β-Turns and their Distortions: A Proposed New Nomenclature, Protein Eng., 3, 479–493.
(
10.1093/protein/3.6.479
) / Protein Eng. by C.M. Wilmott (1990) -
Richardson, J.S. (1981) The Anatomy and Taxonomy of Protein Structure, Adv. Protein Chem., 34, 167–339.
(
10.1016/S0065-3233(08)60520-3
) / Adv. Protein Chem. by J.S. Richardson (1981) -
Milner-White, E.J., Bell, L.H. and Maccallum, P.H. (1992) Pyrrolidine Ring Puckering in cis- and trans-Proline Residues in Proteins and Polypeptides. Different Puckers are Favoured in Certain Situations, J. Mol. Biol., 228, 725–734.
(
10.1016/0022-2836(92)90859-I
) / J. Mol. Biol. by E.J. Milner-White (1992) -
De Leeuw, H.P.M., Haasnoot, C.A.G. and Altona, C. (1980) Empirical Correlations between Conformational Parameters in β-D-Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents, Isr. J. Chem., 20, 108–126.
(
10.1002/ijch.198000059
) / Isr. J. Chem. by H.P.M. De Leeuw (1980) -
Haasnoot, C.A.G., De Leeuw, F.A.A.M., de Leeuw, H.P.M. and Altona, C. (1981) The Relationship between Proton-Proton NMR Coupling Constants and Substituent Electronegativities, Org. Magn. Reson., 15, 43–52.
(
10.1002/mrc.1270150111
) / Org. Magn. Reson. by C.A.G. Haasnoot (1981) - Harris, R.K., Becker, E.D., Bremser, W., Cabral de Menezes, S., Goodfellow, R. and Granger, P. (1997) IUPAC (Commission on Molecular Structure and Spectroscopy, I.5) Recommendations for NMR Nomenclature. A. Nuclear Spin Properties and Conventions for Chemical Shifts (in preparation).
-
Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L. and Sykes, B.D. (1995) 1H, 13C and 15N Chemical Shift Referencing in Biomolecular NMR, J. Biomol. NMR., 6, 135–140.
(
10.1007/BF00211777
) / J. Biomol. NMR. by D.S. Wishart (1995) -
Live, D.H., Davis, D.G., Agosta, W.C. and Cowburn, D. (1984) Long Range Hydrogen Bond Mediated Effects in Peptides: 15N NMR Study of Gramicidin S in Water and Organic Solvents, J. Am. Chem. Soc., 106, 1939–1943.
(
10.1021/ja00319a006
) / J. Am. Chem. Soc. by D.H. Live (1984) - NOE distances may be represented rigorously by notation analogous to that used for J-couplings. However, since protons are always implied, a shorthand notation is widely used: for example, d αN for d HαHN, d NN for d HNHN, d βN for d HβHN, and d αβ for d HαHβ.
-
Williamson, M.P., Havel, T.F. and Wüthrich, K. (1985) Solution Conformation of Proteinase Inhibitor IIA from Bull Seminal Plasma by 1H NMR Spectroscopy and Distance Geometry, J. Mol. Biol., 182, 295–315.
(
10.1016/0022-2836(85)90347-X
) / J. Mol. Biol. by M.P. Williamson (1985) -
Gronenborn, A.M. and Clore, G.M. (1994) Identification of N-Terminal Helix Capping Boxes by Means of 13C Chemical Shifts, J. Biomol. NMR, 4, 455–458.
(
10.1007/BF00179351
) / J. Biomol. NMR by A.M. Gronenborn (1994) -
Eberstadt, M., Gemmecker, G., Mierke, D.F. and Kessler, H. (1995) Scalar Coupling Constants-Their Analysis and their Application for the Elucidation of Structures, Angew. Chem. Int. Ed. Engl., 34, 1671–1695.
(
10.1002/anie.199516711
) / Angew. Chem. Int. Ed. Engl. by M. Eberstadt (1995) -
Ottiger, M., Szyperski, T., Luginbühl, L., Ortenzi, C., Luporini, P., Bradshaw, R.A. and Wüthrich, K. (1994) The NMR Solution Structure of the Pheromone Er-2 from the Ciliated Protozoan Euplotes raikovi, Protein Sci., 3, 1515–1526.
(
10.1002/pro.5560030917
) / Protein Sci. by M. Ottiger (1994) - Saenger, W., (1983) Principles of Nucleic Acid Structure, Springer Verlag, New York, NY, pp. 123–124. / Principles of Nucleic Acid Structure by W. Saenger (1983)
-
Sutcliffe, M.J. (1993) Representing an Ensemble of NMRDerived Protein Structures by a Single Structure, Protein Sci., 2, 936–944.
(
10.1002/pro.5560020607
) / Protein Sci. by M.J. Sutcliffe (1993) -
Fletcher, C.M., Jones, D.N.M., Diamond, R. and Neuhaus, D. (1996) Treatment of NOE Constraints Involving Equivalent or Nonstereoassigned Protons in Calculations of Biomacromolecular Structures, J. Biomol. NMR, 8, 292–310.
(
10.1007/BF00410328
) / J. Biomol. NMR by C.M. Fletcher (1996) -
MacArthur, M.W. and Thornton, J.M. (1993) Conformational Analysis of Protein Structures Derived from NMR Data, Proteins, 17, 232–251.
(
10.1002/prot.340170303
) / Proteins by M.W. MacArthur (1993) -
Hyberts, S.G., Goldberg, M.S., Havel, T.F. and Wagner, G. (1992) The Solution Structure of Eglin c Based on Measurements of Many NOEs and Coupling Constants and its Comparison with X-ray Structures, Protein Sci., 1, 736–751.
(
10.1002/pro.5560010606
) / Protein Sci. by S.G. Hyberts (1992) -
Colovos, C. and Yeates, T.O. (1993) Verification of Protein Structures: Patterns of Nonbonded Atomic Interactions, Protein Sci., 2, 1511–1519.
(
10.1002/pro.5560020916
) / Protein Sci. by C. Colovos (1993) -
Sippl, M.J. (1993) Recognition of Errors in 3–Dimensional Structures of Proteins, Proteins, 17, 355–362.
(
10.1002/prot.340170404
) / Proteins by M.J. Sippl (1993) -
Vriend, G. and Sander, C. (1993) Quality Control of Protein Models: Directional Atomic Contact Analysis, J. Appl. Crystallogr., 26, 47–60.
(
10.1107/S0021889892008240
) / J. Appl. Crystallogr. by G. Vriend (1993) -
MacArthur, M.W., Laskowski, R.A and Thornton, J.M. (1994) Knowledge-Based Validation of Protein-Structure Coordinates Derived by X-ray Crystallography and NMR Spectroscopy, Curr. Opin. Struct. Biol., 4, 731–737.
(
10.1016/S0959-440X(94)90172-4
) / Curr. Opin. Struct. Biol. by M.W. MacArthur (1994) -
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) AQUA and PROCHECK-NMR: Programs for Checking the Quality of Protein Structures Solved by NMR. J. Biomol. NMR, 8, 477–486.
(
10.1007/BF00228148
) / J. Biomol. NMR by R.A. Laskowski (1996) - Jardetzky, O. and Roberts, G.C.K. (1981) NMR in Molecular Biology, Academic Press, New York, NY, pp. 126–142. / NMR in Molecular Biology by O. Jardetzky (1981)
-
Watenpaugh, K.D., Berman, H.M., Bourne, P.E. and Fitzgerald, P.M.D. (1993) The Macromolecular CIF Dictionary, Acta Crystallogr. Ser. A, 49(Supplement), IVI International Congress (IUCr), Abstract OCM-18.02.07.
(
10.1107/S0108767378088364
) - Fitzgerald, P.M.D., Berman, H., Bourne, P. and Watenpaugh, K. (1993) The Macromolecular CIF Dictionary, Abstract No. D008, American Crystallographic Association Annual Meeting, Albuquerque, NM, May 23–28 (available from: http://ndbserver.rutgers.edu:80/mmcif/).
-
Hall, S.R. and Spadaccini, N. (1994) The STAR File: Detailed Specifications, J. Chem. Inf. Comput. Sci., 34, 505–508.
(
10.1021/ci00019a005
) / J. Chem. Inf. Comput. Sci. by S.R. Hall (1994) -
Hall, S.R., Allen, F.H. and Brown, I.D. [International Union of Crystallography, Commission on Crystallographic Data, Commission on Journals, Working Party on Crystallographic Information] (1991) The Crystallographic Information File (CIF): a New Standard Archive File for Crystallography, Acta Crystallogr. Ser. A, 47, 655–685.
(
10.1107/S010876739101067X
) / Acta Crystallogr. Ser. A by S.R. Hall (1991) - International Organization for Standardization (1987) Information Processing Systems-Open Systems Interconnection-Specification of Abstract Syntax Notation One (ASN.1), Technical Report ISO8824.
- International Organization for Standardization (1987) Information Processing Systems-Open Systems Interconnection-Specification of Basic Encoding Rules for Abstract Syntax Notation One (ASN.1), Technical Report ISO8825.
- Ostell, J. (1990) GenInfo ASN.1 Syntax: Sequences, Technical Report 1 & 2, National Center for Biotechnology Information, National Library of Medicine.
- Mockus, J. and Steckert, T.D. (1994) CXF Chemical eXchange Format Version 1.0, Chemical Abstracts Service: Columbus, OH, USA.
- Ulrich, E.L. and Markley, J.L. (1994) A Data Dictionary and Information File for the Exchange and Archiving of NMR Experimental Results, 35th Experimental Nuclear Magnetic Resonance Conference, April 10–15, Asilomar, CA, Abstract WP 112, p. 264. The BioMagResBank web pages (http://www.bmrb.wisc.edu/) contain complete information about this effort including user entry protocols and software.
Dates
Type | When |
---|---|
Created | 22 years, 8 months ago (Dec. 22, 2002, 8:47 a.m.) |
Deposited | 1 month, 3 weeks ago (June 26, 2025, 8:49 a.m.) |
Indexed | 1 day, 16 hours ago (Aug. 21, 2025, 1:53 p.m.) |
Issued | 27 years, 1 month ago (July 1, 1998) |
Published | 27 years, 1 month ago (July 1, 1998) |
Published Print | 27 years, 1 month ago (July 1, 1998) |
@article{Markley_1998, title={Recommendations for the presentation of NMR structures of proteins and nucleic acids – IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy}, volume={12}, ISSN={1573-5001}, url={http://dx.doi.org/10.1023/a:1008290618449}, DOI={10.1023/a:1008290618449}, number={1}, journal={Journal of Biomolecular NMR}, publisher={Springer Science and Business Media LLC}, author={Markley, John L. and Bax, Ad and Arata, Yoji and Hilbers, C. W. and Kaptein, Robert and Sykes, Brian D. and Wright, Peter E. and Wüthrich, Kurt}, year={1998}, month=jul, pages={1–23} }