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ORB, a homology-based program for the prediction of protein NMR chemical shifts (1997)

Gronwald, Wolfram ; Boyko, Robert F. ; Sönnichsen, Frank D. ; [et al.]

Springer

Journal of biomolecular NMR 10 (1997), S. 165-179

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ISSN: 1573-5001

Keywords: Automated sequential assignment ; Homology-based protein NMR chemical shift prediction; ; Protein NMR chemical shift databases ; Multiple alignment

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Abstract A computer program (ORB) has been developed to predict 1H,13C and 15N NMR chemical shifts of previouslyunassigned proteins. The program makes use of the information contained in achemical shift database of previously assigned proteins supplemented by astatistically derived averaged chemical shift database in which the shifts arecategorized according to their residue, atom and secondary structure type[Wishart et al. (1991) J. Mol. Biol., 222, 311–333]. The predictionprocess starts with a multiple alignment of all previously assigned proteinswith the unassigned query protein. ORB uses the sequence and secondarystructure alignment program XALIGN for this task [Wishart et al. (1994)CABIOS, 10, 121–132; 687–688]. The prediction algorithm in ORB isbased on a scoring of the known shifts for each sequence. The scores dependon global sequence similarity, local sequence similarity, structuralsimilarity and residue similarity and determine how much weight one particularshift is given in the prediction process. In situations where no applicablepreviously assigned chemical shifts are available, the shifts derived from theaveraged database are used. In addition to supplying the user with predictedchemical shifts, ORB calculates a confidence value for every prediction. Theseconfidence values enable the user to judge which predictions are the mostaccurate and they are particularly useful when ORB is incorporated into acomplete autoassignment package. The usefulness of ORB was tested on threemedium-sized proteins: an interleukin-8 analog, a troponin C synthetic peptideheterodimer and cardiac troponin C. Excellent results are obtained if ORB isable to use the chemical shifts of at least one highly homologous sequence.ORB performs well as long as the sequence identity between proteins with knownchemical shifts and the new sequence is not less than 30%.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1018389332160

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Synthese mittlerer und großer Ringe, XXIII. Photochemische Umlagerung von 3,6-Alkanooxepin-4,5-dicarbonsäureestern (1989)

Tochtermann, Werner ; Olsson, Gesa ; Sczostak, Axel ; [et al.]

Weinheim : Wiley-Blackwell

Berichte der deutschen chemischen Gesellschaft 122 (1989), S. 199-207

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ISSN: 0009-2940

Keywords: 3,6-Alkanooxepine-4,5-dicarboxylic esters ; Methanohydroazulene derivatives ; Photochemical rearrangement ; Tricycloalkene derivatives ; Chemistry ; Inorganic Chemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Description / Table of Contents: Synthesis of Medium and Large Rings, XXIII. Photochemical Rearrangement of 3,6-Alkanooxepine-4,5-dicarboxylic EstersIrradiation of the 3,6-alkanooxepine-4,5-dicarboxylic esters 1a-d affords the tricyclic aldehydes 2a-d, the constitutions of which were determined by X-ray structural analysis of 2a and 2d. The disubstituted 3,6-decanooxepine 1e gives in low yield the bridged dihydrofuran 4b, whose structure was also established by X-ray analysis. Mechanistic investigations show, that the photochemical rearrangement 1 → 2 takes place via dihydrofurans 3, cyclopropane carbaldehydes 6, and cyclopentadienecarbaldehydes 7.

Notes: Bestrahlung der 3,6-Alkanooxepin-4,5-dicarbonsäureester 1a-d liefert die tricyclischen Aldehyde 2a-d, deren Konstitutionen durch Röntgenstrukturanalyse von 2a und 2d gesichert wurden. Das analoge disubstituierte 3,6-Decanooxepin 1e führt unter anderem zum überbrückten Dihydrofuran 4b, für das ebenfalls eine Röntgenstrukturanalyse vorliegt. Mechanistische Untersuchungen zeigen, daß die Photoumlagerung 1 → 2 über Dihydrofurane 3, Cyclopropancarbaldehyde 6 und Cyclopentadiencarbaldehyde 7 verläuft.

Additional Material: 2 Ill.