Literature DB >> 24831340

Automatic NOESY assignment in CS-RASREC-Rosetta.

Oliver F Lange1.   

Abstract

We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calculations with algorithms for automatic NOE assignment. The method was applied to two proteins in the 15-20 kDa size range for which both, NMR and X-ray data, is available. The autoNOE-Rosetta calculations converge for both proteins and yield accurate structures with an RMSD of 1.9 Å to the X-ray reference structures. The method greatly expands the radius of convergence for automatic NOE assignment, and should be broadly useful for NMR structure determination.

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Year:  2014        PMID: 24831340     DOI: 10.1007/s10858-014-9833-3

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


  25 in total

1.  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

2.  Correction of spin diffusion during iterative automated NOE assignment.

Authors:  Jens P Linge; Michael Habeck; Wolfgang Rieping; Michael Nilges
Journal:  J Magn Reson       Date:  2004-04       Impact factor: 2.229

3.  Consistent blind protein structure generation from NMR chemical shift data.

Authors:  Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H Arrowsmith; Thomas Szyperski; Gaetano T Montelione; David Baker; Ad Bax
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-07       Impact factor: 11.205

4.  Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA.

Authors:  P Güntert; W Braun; K Wüthrich
Journal:  J Mol Biol       Date:  1991-02-05       Impact factor: 5.469

5.  Improving 3D structure prediction from chemical shift data.

Authors:  Gijs van der Schot; Zaiyong Zhang; Robert Vernon; Yang Shen; Wim F Vranken; David Baker; Alexandre M J J Bonvin; Oliver F Lange
Journal:  J Biomol NMR       Date:  2013-08-03       Impact factor: 2.835

6.  Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker.

Authors:  Robert Vernon; Yang Shen; David Baker; Oliver F Lange
Journal:  J Biomol NMR       Date:  2013-08-22       Impact factor: 2.835

7.  Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors:  A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-09-01

8.  A calculation strategy for the structure determination of symmetric dimers by 1H NMR.

Authors:  M Nilges
Journal:  Proteins       Date:  1993-11

9.  NMR structure determination for larger proteins using backbone-only data.

Authors:  Srivatsan Raman; Oliver F Lange; Paolo Rossi; Michael Tyka; Xu Wang; James Aramini; Gaohua Liu; Theresa A Ramelot; Alexander Eletsky; Thomas Szyperski; Michael A Kennedy; James Prestegard; Gaetano T Montelione; David Baker
Journal:  Science       Date:  2010-02-04       Impact factor: 47.728

10.  Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation.

Authors:  Oliver F Lange; David Baker
Journal:  Proteins       Date:  2012-03
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  7 in total

1.  Structure determination of uniformly (13)C, (15)N labeled protein using qualitative distance restraints from MAS solid-state (13)C-NMR observed paramagnetic relaxation enhancement.

Authors:  Hajime Tamaki; Ayako Egawa; Kouki Kido; Tomoshi Kameda; Masakatsu Kamiya; Takashi Kikukawa; Tomoyasu Aizawa; Toshimichi Fujiwara; Makoto Demura
Journal:  J Biomol NMR       Date:  2016-01-04       Impact factor: 2.835

2.  Interleukin-37 monomer is the active form for reducing innate immunity.

Authors:  Elan Z Eisenmesser; Adrian Gottschlich; Jasmina S Redzic; Natasia Paukovich; Jay C Nix; Tania Azam; Lingdi Zhang; Rui Zhao; Jeffrey S Kieft; Erlinda The; Xianzhong Meng; Charles A Dinarello
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-28       Impact factor: 11.205

Review 3.  Chemical shift-based methods in NMR structure determination.

Authors:  Santrupti Nerli; Andrew C McShan; Nikolaos G Sgourakis
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2018-03-11       Impact factor: 9.795

4.  The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.

Authors:  Antonio Rosato; Wim Vranken; Rasmus H Fogh; Timothy J Ragan; Roberto Tejero; Kari Pederson; Hsiau-Wei Lee; James H Prestegard; Adelinda Yee; Bin Wu; Alexander Lemak; Scott Houliston; Cheryl H Arrowsmith; Michael Kennedy; Thomas B Acton; Rong Xiao; Gaohua Liu; Gaetano T Montelione; Geerten W Vuister
Journal:  J Biomol NMR       Date:  2015-06-14       Impact factor: 2.835

Review 5.  Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Authors:  Julia Koehler Leman; Brian D Weitzner; Steven M Lewis; Jared Adolf-Bryfogle; Nawsad Alam; Rebecca F Alford; Melanie Aprahamian; David Baker; Kyle A Barlow; Patrick Barth; Benjamin Basanta; Brian J Bender; Kristin Blacklock; Jaume Bonet; Scott E Boyken; Phil Bradley; Chris Bystroff; Patrick Conway; Seth Cooper; Bruno E Correia; Brian Coventry; Rhiju Das; René M De Jong; Frank DiMaio; Lorna Dsilva; Roland Dunbrack; Alexander S Ford; Brandon Frenz; Darwin Y Fu; Caleb Geniesse; Lukasz Goldschmidt; Ragul Gowthaman; Jeffrey J Gray; Dominik Gront; Sharon Guffy; Scott Horowitz; Po-Ssu Huang; Thomas Huber; Tim M Jacobs; Jeliazko R Jeliazkov; David K Johnson; Kalli Kappel; John Karanicolas; Hamed Khakzad; Karen R Khar; Sagar D Khare; Firas Khatib; Alisa Khramushin; Indigo C King; Robert Kleffner; Brian Koepnick; Tanja Kortemme; Georg Kuenze; Brian Kuhlman; Daisuke Kuroda; Jason W Labonte; Jason K Lai; Gideon Lapidoth; Andrew Leaver-Fay; Steffen Lindert; Thomas Linsky; Nir London; Joseph H Lubin; Sergey Lyskov; Jack Maguire; Lars Malmström; Enrique Marcos; Orly Marcu; Nicholas A Marze; Jens Meiler; Rocco Moretti; Vikram Khipple Mulligan; Santrupti Nerli; Christoffer Norn; Shane Ó'Conchúir; Noah Ollikainen; Sergey Ovchinnikov; Michael S Pacella; Xingjie Pan; Hahnbeom Park; Ryan E Pavlovicz; Manasi Pethe; Brian G Pierce; Kala Bharath Pilla; Barak Raveh; P Douglas Renfrew; Shourya S Roy Burman; Aliza Rubenstein; Marion F Sauer; Andreas Scheck; William Schief; Ora Schueler-Furman; Yuval Sedan; Alexander M Sevy; Nikolaos G Sgourakis; Lei Shi; Justin B Siegel; Daniel-Adriano Silva; Shannon Smith; Yifan Song; Amelie Stein; Maria Szegedy; Frank D Teets; Summer B Thyme; Ray Yu-Ruei Wang; Andrew Watkins; Lior Zimmerman; Richard Bonneau
Journal:  Nat Methods       Date:  2020-06-01       Impact factor: 28.547

6.  Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.

Authors:  Thomas Evangelidis; Santrupti Nerli; Jiří Nováček; Andrew E Brereton; P Andrew Karplus; Rochelle R Dotas; Vincenzo Venditti; Nikolaos G Sgourakis; Konstantinos Tripsianes
Journal:  Nat Commun       Date:  2018-01-26       Impact factor: 14.919

7.  De novo design of a non-local β-sheet protein with high stability and accuracy.

Authors:  Enrique Marcos; Tamuka M Chidyausiku; Andrew C McShan; Thomas Evangelidis; Santrupti Nerli; Lauren Carter; Lucas G Nivón; Audrey Davis; Gustav Oberdorfer; Konstantinos Tripsianes; Nikolaos G Sgourakis; David Baker
Journal:  Nat Struct Mol Biol       Date:  2018-10-29       Impact factor: 15.369

  7 in total

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