Literature DB >> 25801209

Combined automated NOE assignment and structure calculation with CYANA.

Peter Güntert1,2,3, Lena Buchner4.   

Abstract

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.

Keywords:  Automated assignment; CASD-NMR; CYANA; Distance restraints; NOESY; Structure calculation

Mesh：

Substances：

Year:  2015        PMID： 25801209     DOI： 10.1007/s10858-015-9924-9

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


  42 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.

Authors:  JunGoo Jee; Peter Güntert
Journal:  J Struct Funct Genomics       Date:  2003

3.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

4.  Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).

Authors:  Wolfram Gronwald; Sherif Moussa; Ralph Elsner; Astrid Jung; Bernhard Ganslmeier; Jochen Trenner; Werner Kremer; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2002-08       Impact factor: 2.835

5.  Exclusively NOESY-based automated NMR assignment and structure determination of proteins.

Authors:  Teppei Ikeya; Jun-Goo Jee; Yoshiki Shigemitsu; Junpei Hamatsu; Masaki Mishima; Yutaka Ito; Masatsune Kainosho; Peter Güntert
Journal:  J Biomol NMR       Date:  2011-03-30       Impact factor: 2.835

6.  Automated combined assignment of NOESY spectra and three-dimensional protein structure determination.

Authors:  C Mumenthaler; P Güntert; W Braun; K Wüthrich
Journal:  J Biomol NMR       Date:  1997-12       Impact factor: 2.835

7.  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

8.  Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.

Authors:  M Nilges
Journal:  J Mol Biol       Date:  1995-02-03       Impact factor: 5.469

9.  Torsion angle dynamics for NMR structure calculation with the new program DYANA.

Authors:  P Güntert; C Mumenthaler; K Wüthrich
Journal:  J Mol Biol       Date:  1997-10-17       Impact factor: 5.469

10.  Atomic-resolution three-dimensional structure of amyloid β fibrils bearing the Osaka mutation.

Authors:  Anne K Schütz; Toni Vagt; Matthias Huber; Oxana Y Ovchinnikova; Riccardo Cadalbert; Joseph Wall; Peter Güntert; Anja Böckmann; Rudi Glockshuber; Beat H Meier
Journal:  Angew Chem Int Ed Engl       Date:  2014-11-13       Impact factor: 15.336
View more
  106 in total

1.  The Exact NOE as an Alternative in Ensemble Structure Determination.

Authors:  Beat Vögeli; Simon Olsson; Peter Güntert; Roland Riek
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

2.  Heterochiral Knottin Protein: Folding and Solution Structure.

Authors:  Surin K Mong; Frank V Cochran; Hongtao Yu; Zachary Graziano; Yu-Shan Lin; Jennifer R Cochran; Bradley L Pentelute
Journal:  Biochemistry       Date:  2017-10-17       Impact factor: 3.162

3.  The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework.

Authors:  Lau D Nielsen; Mads M Foged; Anastasia Albert; Andreas B Bertelsen; Cecilie L Søltoft; Samuel D Robinson; Steen V Petersen; Anthony W Purcell; Baldomero M Olivera; Raymond S Norton; Terje Vasskog; Helena Safavi-Hemami; Kaare Teilum; Lars Ellgaard
Journal:  J Biol Chem       Date:  2019-04-11       Impact factor: 5.157

4.  Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.

Authors:  Julia M Würz; Peter Güntert
Journal:  J Biomol NMR       Date:  2017-02-03       Impact factor: 2.835

5.  Structural investigation of glycan recognition by the ERAD quality control lectin Yos9.

Authors:  Andreas Kniss; Sina Kazemi; Frank Löhr; Maren Berger; Vladimir V Rogov; Peter Güntert; Thomas Sommer; Ernst Jarosch; Volker Dötsch
Journal:  J Biomol NMR       Date:  2018-07-31       Impact factor: 2.835

6.  NMR model structure of the antimicrobial peptide maximin 3.

Authors:  Silvia Benetti; Patrick Brendan Timmons; Chandralal M Hewage
Journal:  Eur Biophys J       Date:  2019-02-08       Impact factor: 1.733

7.  Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

Authors:  Qin Shu; Andrzej M Krezel; Zachary T Cusumano; Jerome S Pinkner; Roger Klein; Scott J Hultgren; Carl Frieden
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-13       Impact factor: 11.205

8.  S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.

Authors:  Cédric Eichmann; Christos Tzitzilonis; Tomohiro Nakamura; Witek Kwiatkowski; Innokentiy Maslennikov; Senyon Choe; Stuart A Lipton; Roland Riek
Journal:  J Mol Biol       Date:  2016-07-27       Impact factor: 5.469

9.  Structural insights into TAZ2 domain-mediated CBP/p300 recruitment by transactivation domain 1 of the lymphopoietic transcription factor E2A.

Authors:  Marina R Lochhead; Alexandra D Brown; Alyssa C Kirlin; Seth Chitayat; Kim Munro; Jane E Findlay; George S Baillie; David P LeBrun; David N Langelaan; Steven P Smith
Journal:  J Biol Chem       Date:  2020-02-25       Impact factor: 5.157

10.  Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril.

Authors:  Marielle Aulikki Wälti; Francesco Ravotti; Hiromi Arai; Charles G Glabe; Joseph S Wall; Anja Böckmann; Peter Güntert; Beat H Meier; Roland Riek
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-28       Impact factor: 11.205
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.