Literature DB >> 15103611

DRESS: a database of REfined solution NMR structures.

Sander B Nabuurs1, Aart J Nederveen, Wim Vranken, Jurgen F Doreleijers, Alexandre M J J Bonvin, Geerten W Vuister, Gert Vriend, Christian A E M Spronk.   

Abstract

Several studies have shown that biomolecular NMR structures are often of lower quality when compared to crystal structures, and consequently they are often excluded from structural analyses. We present a publicly available database of re-refined NMR structures, exhibiting significantly improved quality. This database (available at http://www.cmbi.kun.nl/dress/) presents a uniformly refined and validated set of structural models that improves the value of these NMR structures as input for experimental and theoretical studies in many fields of research. Copyright 2004 Wiley-Liss, Inc.

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Year:  2004        PMID: 15103611     DOI: 10.1002/prot.20118

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  45 in total

1.  Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.

Authors:  Mark Berjanskii; Jianjun Zhou; Yongjie Liang; Guohui Lin; David S Wishart
Journal:  J Biomol NMR       Date:  2012-06-08       Impact factor: 2.835

2.  Definition of a new information-based per-residue quality parameter.

Authors:  Sander B Nabuurs; Elmar Krieger; Chris A E M Spronk; Aart J Nederveen; Gert Vriend; Geerten W Vuister
Journal:  J Biomol NMR       Date:  2005-10       Impact factor: 2.835

3.  Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1.

Authors:  Ming Li; Hemali P Phatnani; Ziqiang Guan; Harvey Sage; Arno L Greenleaf; Pei Zhou
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-28       Impact factor: 11.205

4.  BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures.

Authors:  Jurgen F Doreleijers; Aart J Nederveen; Wim Vranken; Jundong Lin; Alexandre M J J Bonvin; Robert Kaptein; John L Markley; Eldon L Ulrich
Journal:  J Biomol NMR       Date:  2005-05       Impact factor: 2.835

5.  AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.

Authors:  Wolfram Gronwald; Konrad Brunner; Renate Kirchhöfer; Jochen Trenner; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2006-11-29       Impact factor: 2.835

6.  Structure, interactions, and dynamics of the RING domain from human TRAF6.

Authors:  Pascal Mercier; Michael J Lewis; D Duong Hau; Linda F Saltibus; Wei Xiao; Leo Spyracopoulos
Journal:  Protein Sci       Date:  2007-02-27       Impact factor: 6.725

7.  Structural characterization reveals that a PilZ domain protein undergoes substantial conformational change upon binding to cyclic dimeric guanosine monophosphate.

Authors:  Jae-Sun Shin; Kyoung-Seok Ryu; Junsang Ko; Arum Lee; Byong-Seok Choi
Journal:  Protein Sci       Date:  2010-12-23       Impact factor: 6.725

8.  Predicting 13Calpha chemical shifts for validation of protein structures.

Authors:  Jorge A Vila; Myriam E Villegas; Hector A Baldoni; Harold A Scheraga
Journal:  J Biomol NMR       Date:  2007-06-09       Impact factor: 2.835

9.  Solution structure of the Ubp-M BUZ domain, a highly specific protein module that recognizes the C-terminal tail of free ubiquitin.

Authors:  Ming-Tao Pai; Shiou-Ru Tzeng; Jeffrey J Kovacs; Mignon A Keaton; Shawn S-C Li; Tso-Pang Yao; Pei Zhou
Journal:  J Mol Biol       Date:  2007-04-12       Impact factor: 5.469

10.  The war of tools: how can NMR spectroscopists detect errors in their structures?

Authors:  Edoardo Saccenti; Antonio Rosato
Journal:  J Biomol NMR       Date:  2008-03-05       Impact factor: 2.835

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