Literature DB >> 12815260

IBIS--a tool for automated sequential assignment of protein spectra from triple resonance experiments.

Sven G Hyberts1, Gerhard Wagner.   

Abstract

We have developed a tool for computer-assisted assignments of protein NMR spectra from triple resonance data. The program is designed to resemble established manual assignment procedures as closely as possible. IBIS exports its results in XEASY format. Thus, using IBIS the operator has continuous visual and accounting control over the progress of the assignment procedure. IBIS achieves complete assignments for those residues that exhibit sequential triple resonance connectivities within a few hours or days.

Mesh：

Year:  2003        PMID： 12815260     DOI： 10.1023/a:1024078926886

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  28 in total

1.  Efficient analysis of protein 2D NMR spectra using the software package EASY.

Authors:  C Eccles; P Güntert; M Billeter; K Wüthrich
Journal:  J Biomol NMR       Date:  1991-07       Impact factor: 2.835

2.  A computer-based protocol for semiautomated assignments and 3D structure determination of proteins.

Authors:  R P Meadows; E T Olejniczak; S W Fesik
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

3.  Amino-acid-type identification for deuterated proteins with a beta-carbon-edited HNCOCACB experiment.

Authors:  V Dötsch; H Matsuo; G Wagner
Journal:  J Magn Reson B       Date:  1996-07

4.  Automated analysis of protein NMR assignments using methods from artificial intelligence.

Authors:  D E Zimmerman; C A Kulikowski; Y Huang; W Feng; M Tashiro; S Shimotakahara; C Chien; R Powers; G T Montelione
Journal:  J Mol Biol       Date:  1997-06-20       Impact factor: 5.469

5.  The program XEASY for computer-supported NMR spectral analysis of biological macromolecules.

Authors:  C Bartels; T H Xia; M Billeter; P Güntert; K Wüthrich
Journal:  J Biomol NMR       Date:  1995-07       Impact factor: 2.835

6.  Use of fuzzy mathematics for complete automated assignment of peptide 1H 2D NMR spectra.

Authors:  J Xu; S K Straus; B C Sanctuary; L Trimble
Journal:  J Magn Reson B       Date:  1994-01

7.  Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence.

Authors:  D Zimmerman; C Kulikowski; L Wang; B Lyons; G T Montelione
Journal:  J Biomol NMR       Date:  1994-03       Impact factor: 2.835

8.  Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Basic pancreatic trypsin inhibitor.

Authors:  G Wagner; K Wüthrich
Journal:  J Mol Biol       Date:  1982-03-05       Impact factor: 5.469

9.  Automated backbone assignment of labeled proteins using the threshold accepting algorithm.

Authors:  M Leutner; R M Gschwind; J Liermann; C Schwarz; G Gemmecker; H Kessler
Journal:  J Biomol NMR       Date:  1998-01       Impact factor: 2.835

10.  Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

Authors:  P J Kraulis
Journal:  J Mol Biol       Date:  1994-11-04       Impact factor: 5.469
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  24 in total

Review 1.  Resolution and sensitivity of high field nuclear magnetic resonance spectroscopy.

Authors:  D Rovnyak; J C Hoch; A S Stern; G Wagner
Journal:  J Biomol NMR       Date:  2004-09       Impact factor: 2.835

2.  SAGA: rapid automatic mainchain NMR assignment for large proteins.

Authors:  Gordon M Crippen; Aikaterini Rousaki; Matthew Revington; Yongbo Zhang; Erik R P Zuiderweg
Journal:  J Biomol NMR       Date:  2010-03-16       Impact factor: 2.835

3.  Letter to the Editor: Rapid backbone (1)H, (13)C, and (15)N assignment of the V1 domain of human PKC iota using the new program IBIS.

Authors:  Michael H A Roehrl; Sven G Hyberts; Zhen-Yu Jim Sun; Alan P Fields; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2003-08       Impact factor: 2.835

4.  EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.

Authors:  Erik R P Zuiderweg; Ireena Bagai; Paolo Rossi; Eric B Bertelsen
Journal:  J Biomol NMR       Date:  2013-10       Impact factor: 2.835

5.  Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO).

Authors:  Hamid R Eghbalnia; Arash Bahrami; Liya Wang; Amir Assadi; John L Markley
Journal:  J Biomol NMR       Date:  2005-07       Impact factor: 2.835

6.  PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach.

Authors:  Yizhuang Xu; Xiaoxia Wang; Jun Yang; Julia Vaynberg; Jun Qin
Journal:  J Biomol NMR       Date:  2006-01       Impact factor: 2.835

7.  KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.

Authors:  Naohiro Kobayashi; Junji Iwahara; Seizo Koshiba; Tadashi Tomizawa; Naoya Tochio; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Journal:  J Biomol NMR       Date:  2007-07-18       Impact factor: 2.835

8.  Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm.

Authors:  Roland Schmucki; Shigeyuki Yokoyama; Peter Güntert
Journal:  J Biomol NMR       Date:  2008-11-26       Impact factor: 2.835

9.  Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [ (1)H, (1)H]-NOESY.

Authors:  Francesco Fiorito; Torsten Herrmann; Fred F Damberger; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2008-08-16       Impact factor: 2.835

10.  A practical implementation of cross-spectrum in protein backbone resonance assignment.

Authors:  Kang Chen; Frank Delaglio; Nico Tjandra
Journal:  J Magn Reson       Date:  2009-12-24       Impact factor: 2.229
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