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references therein
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Revised Recommendations 1971; reprinted in the Compendium (ref. 9)
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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).
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reprinted in the Compendium (ref. 9)
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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).
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BioMagResBank (http://www.bmrb.wisc.edu) and the NCSA Biology Workbench (http://biology.ncsa.uiuc.edu)
-
Access to various databases (e.g., GenBank, DDBJ, EBI (EMBL), EC Enzyme Data Bank, PIR, SWISS-PROT, PRF, PDB, NDB, BMRB) is provided over the Internet. Useful compilations of Internet addresses are found, for example, on the home pages of the Protein Data Bank (http://www.pdb.bnl.gov/), BioMagResBank (http://www.bmrb.wisc.edu) and the NCSA Biology Workbench (http://biology.ncsa.uiuc.edu).
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84912613243
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Recommendations 1992, Academic Press, Orlando, FL, U.S.A.
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International Union of Biochemistry and Molecular Biology (1992) Enzyme Nomenclature, Recommendations 1992, Academic Press, Orlando, FL, U.S.A.
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Enzyme Nomenclature
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20
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2342547519
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Chemical Abstracts Service, Columbus, OH, U.S.A. (http://info.cas.org/).
-
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21
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Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains, Tentative Rules 1969
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reprinted in the Compendium (ref. 9)
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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).
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Nomenclature and Symbolism for Amino Acids and Peptides, Recommendations 1983
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reprinted in the Compendium (ref. 9)
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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).
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84988072575
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Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains, Recommendations 1982
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reprinted in the Compendium (ref. 9)
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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).
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Eur. J. Biochem.
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25
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2342493233
-
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note
-
The 1983 recommendations (ref. 21) specified the use of numbers to designate atoms and the use of the R/S rules of Cahn, Ingold and Prelog (refs. 25 and 26, see also refs. 27-29) to define stereochemistry. According to the R/S rules, a tetrahedral carbon X with prochiral substituents A > B > C = C′ (where the priority is according to decreasing atomic mass and C and C′ have equivalent mass and are labeled arbitrarily) is labeled as follows: one sights down the A-X axis and assumes that C′ takes precedence over C (as it would if it were replaced, for example, with a heavier isotope). Then, if B, C′, and C (projecting away from the viewer) are clockwise, C′ is labeled as pro-R and C is labeled as pro-S; if they are counterclockwise, C′ is labeled as pro-S and C is labeled as pro-R.
-
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-
-
26
-
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84981828672
-
Specification of Molecular Chirality
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Cahn, R.S., Ingold, C.K. and Prelog, V. (1966) Specification of Molecular Chirality, Angew. Chem. Int. Ed. Engl., 5, 385-415; 511.
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Cahn, R.S.1
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Prelog, V.3
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27
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0020169638
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Basic Principles of the CIP-System and Proposals for a Revision
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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.
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Prelog, V.1
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28
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9244265014
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Unambiguous Specification of Stereoisomerism about a Double Bond
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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.
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29
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Unique and Unambiguous Specification of Stereoisomerism about a Double Bond in Nomenclature and Other Notation Systems
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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.
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30
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84961486593
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Nomenclature of Organic Chemistry, Section E: Stereochemistry
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Recommendations 1974 (1976); reprinted in the Compendium (ref. 9)
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IUPAC Commission on Nomenclature of Organic Chemistry (CNOC) (1976) Nomenclature of Organic Chemistry, Section E: Stereochemistry, Recommendations 1974, Pure Appl. Chem., 45, 11-30 (1976); reprinted in the Compendium (ref. 9).
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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.
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note
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Since the experimental NOEs involve distances to the individual protons rather than to the reference point of the pseudoatom, NOE distance constraints involving pseudoatoms must contain a correction factor. A conservative and straight-forward approach is to set these corrections equal to the distance between the reference point of the pseudoatom and the protons that it replaces. Tables listing these corrections for the common amino acid residues have been published (refs. 30 and 33) as well as more refined corrections (for example, see refs. 32 and 34).
-
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33
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44949290542
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Calculation of the Nuclear Overhauser Effect and Determination of Proton-Proton Distances in the Presence of Internal Motions
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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.
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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.
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Straightening out the Dihedral Angles
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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.
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Wilmott, C.M. and Thornton, J.M. (1990) β-Turns and their Distortions: A Proposed New Nomenclature, Protein Eng., 3, 479-493.
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Empirical Correlations between Conformational Parameters in β-D-Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents
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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.
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Sykes, B.D.8
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2342496112
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note
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DSS = 0.0246 ppm (i.e., to high frequency from that of DSS).
-
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46
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-
2342605880
-
-
note
-
2H signals of a water sample at 298 K as measured by Dr. Frits Abildgaard and David M. LeMaster at the National Magnetic Resonance Facility at Madison. This value is a surrogate for the isotopomers of DSS, and its derivation assumes that there is no primary isotope effect on the ratio.
-
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47
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-
2342555510
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-
note
-
2O solution containing 10% trimethylphosphate as the indirect reference and DSS as the direct reference.
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48
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2342661070
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note
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HαHβ.
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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.
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The NMR Solution Structure of the Pheromone Er-2 from the Ciliated Protozoan Euplotes raikovi
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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.
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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.
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