caa a22 4500 47713615X CHVBK 20180405111718.0 cr unu---uuuuu 170330e19970901xx s 000 0 eng 10.1023/A:1018389332160 doi (NATIONALLICENCE)springer-10.1023/A:1018389332160 ORB, a homology-based program for the prediction of protein NMR chemical shifts [Elektronische Daten] [Wolfram Gronwald, Robert Boyko, Frank Sönnichsen, David Wishart, Brian Sykes] 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%. Kluwer Academic Publishers, 1997 Automated sequential assignment nationallicence Homology-based protein NMR chemical shift prediction nationallicence Protein NMR chemical shift databases nationallicence Multiple alignment nationallicence Gronwald Wolfram Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut Boyko Robert Department of Biochemistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada aut Sönnichsen Frank Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, U.S.A aut Wishart David Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut Sykes Brian Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut Journal of Biomolecular NMR Kluwer Academic Publishers 10/2(1997-09-01), 165-179 0925-2738 10:2<165 1997 10 10858 https://doi.org/10.1023/A:1018389332160 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1023/A:1018389332160 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Gronwald Wolfram Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut NATIONALLICENCE 700 1- Boyko Robert Department of Biochemistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada aut NATIONALLICENCE 700 1- Sönnichsen Frank Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, U.S.A aut NATIONALLICENCE 700 1- Wishart David Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut NATIONALLICENCE 700 1- Sykes Brian Protein Engineering Network of Centres of Excellence, University of Alberta, 713 Heritage Medical Research Centre, T6G 2S2, Edmonton, AB, Canada aut NATIONALLICENCE 773 0- Journal of Biomolecular NMR Kluwer Academic Publishers 10/2(1997-09-01), 165-179 0925-2738 10:2<165 1997 10 10858 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer