Some uses of a best molecular fit routine

Nyburg, S. C.

doi:10.1107/s0567740874002603

Cited by 142 publications

(24 citation statements)

References 3 publications

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“…Cluster analysis was used on the distance matrix, as a unit-variable matrix [13], calculated between all pairs of structures (root-mean-square coordinate deviation, RMSD) [14], considering the position of all atoms with the exception of the side chain. As a consequence, the distance values actually used by the algorithm are more correctly interpreted as secondary distances; the validity of this approach was demonstrated in many fields of application [15,16] and it is very useful to sort out patterns embedded in a data field.…”

Section: Resultsmentioning

confidence: 99%

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

et al. 1995

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The absolute configuration of fusaproliferin, a toxic metabolite produced by Fusarium proliferaturn, was determined by the combined use of 1H NMR and distance geometry. The configuration of double bonds has been determined in agreement with NOESY buildup data. An R configuration for C10 was determined using Mosher's method. Processing the constraints obtained from NOESY experiments with a distance geometry program, a limited number (80) of possible structures was derived. An agglomerative nonhierarchical method of clustering was used in order to place these structures into classes suggested by the data, and not previously defined in any way. This statistical method showed that indeed the structures could be grouped in four classes. One of these classes is represented by a single structure, with the highest sum of violations and was discarded. All other structures have the same chirality; respectively S for C14 and R for C15. In solution the overall conformation is quite well defined in the region of the five-member ring and the planes of double bonds C2--C3 and C11--C12, while near to C8 and C9 internal flexibility appears evident.

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Section: Resultsmentioning

confidence: 99%

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

et al. 1995

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“…Phenindione was used as the reference, and the two enantiomers of warfarin were translated so that the centroid of the atoms to be fitted was superimposed on the centroid of the corresponding atoms in phenindione. The warfarin enantiomers were then rotated about this point to obtain the best possible fit between the specified pairs of atoms (Nyburg, 1974). The atoms used to match the structures are shown by asterisks in Fig.…”

Section: The Role Of T-cells In Drug Hypersensitivitymentioning

confidence: 99%

Characterization of the T-Cell Response in a Patient with Phenindione Hypersensitivity

Naisbitt¹,

Farrell²,

Chamberlain³

et al. 2005

J Pharmacol Exp Ther

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The oral anticoagulant phenindione [2-phenyl-1H-indene-1,3(2H)-dione] is associated with hypersensitivity reactions in 1.5 to 3% of patients, the pathogenesis of which is unclear. We describe a patient who developed a severe hypersensitivity reaction that involved both the skin and lungs. A lymphocyte transformation test showed proliferation of T-cells from the hypersensitive patient, but not from four controls on exposure to phenindione in vitro. Drug-specific T-cell clones were generated and characterized in terms of their phenotype, functionality, and mechanism of antigen presentation. Forty-three human leukocyte antigen class II restricted CD4ϩ ␣␤ T-cell clones were identified. T-cell activation resulted in the secretion of interferon-␥ and interleukin-5. Five of seven clones proliferated with phenindione alone, whereas two clones also proliferated with 2-phenylindene. Certain T-cell clones were also stimulated by R-and S-warfarin; computer modeling revealed that warfarin can adopt a phenindione-like structure. Phenindione was presented to T-cells via two pathways: first, bound directly to major histocompatibility complex and second, bound to a processed peptide. Our data show that CD4 ϩ T-cells are involved in the pathophysiology of phenindione hypersensitivity. There may be cross-sensitivity with warfarin in some phenindione hypersensitive patients.

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“…Sämtliche Phos- Tabelle 5. f-Bu 6 P 8 . Kontrolle der Molekülsymmetrie 2/m (Analyse mit dem Programm BMFIT (Nyburg, 1974;Yuen et al, 1979); angegeben ist jeweils die Summe der quadratischen Abweichungen Σ Δ 2 [Α 2 ] nach der Anpassung beider Molekülhälften)…”

Section: Beschreibung Der Struktur Und Diskussionunclassified

Beiträge zur Strukturchemie phosphorhaltiger Ketten und Ringe, IV*. Die Kristall- und Molekülstruktur des Bicyclotetraphosphans t-Bu₆P₈

Fehér¹,

Fröhlich²,

Tebbe³

1982

Zeitschrift Für Kristallographie - Crystalline Materials

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The bicyclic phosphorus compound 2,2',3,3',4,4'-Hexa(ferf-butyl)-1,1'-bicyclotetraphosphane /-Bu 6 P 8 , C 24 H 54 P 8 , crystallizes at room temperature in the monoclinic space group P2 1 jn (No. 14) with a = 1141.6(3)pm, b = 1805.7(2)pm, c = 1764.8(3)pm, β = 108.32(2)° and Ζ = 4 formula units. The crystal structure has been solved by 'direct methods' and refined to R = 0.076 with 5361 independent reflections.The molecule with approximate symmetry C 2h consists of two σ-bonded, trans positioned and slightly folded four-membered rings of phosphorus atoms. The exocyclic bridge between the two rings [

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Some uses of a best molecular fit routine

Abstract: A program is described which gives the best least‐squares fit between two sets of atoms. Various possible uses of the program are discussed.

Cited by 142 publications

References 3 publications

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

Characterization of the T-Cell Response in a Patient with Phenindione Hypersensitivity

Beiträge zur Strukturchemie phosphorhaltiger Ketten und Ringe, IV*. Die Kristall- und Molekülstruktur des Bicyclotetraphosphans t-Bu₆P₈

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Some uses of a best molecular fit routine

Abstract: A program is described which gives the best least‐squares fit between two sets of atoms. Various possible uses of the program are discussed.

Cited by 142 publications

References 3 publications

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

Characterization of the T-Cell Response in a Patient with Phenindione Hypersensitivity

Beiträge zur Strukturchemie phosphorhaltiger Ketten und Ringe, IV*. Die Kristall- und Molekülstruktur des Bicyclotetraphosphans t-Bu6P8

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Beiträge zur Strukturchemie phosphorhaltiger Ketten und Ringe, IV*. Die Kristall- und Molekülstruktur des Bicyclotetraphosphans t-Bu₆P₈