Literature DB >> 24060334

Quality assessment of protein NMR structures.

Antonio Rosato1, Roberto Tejero, Gaetano T Montelione.   

Abstract

Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These quality assessment metrics and standards will aid NMR spectroscopists in determining more accurate structures, and increase the value and utility of these structures for the broad scientific community.
Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2013        PMID: 24060334      PMCID: PMC4110634          DOI: 10.1016/j.sbi.2013.08.005

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  74 in total

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5.  Assessing model accuracy using the homology modeling automatically software.

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Authors:  L Zhu; H J Dyson; P E Wright
Journal:  J Biomol NMR       Date:  1998-01       Impact factor: 2.835

7.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

8.  Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications.

Authors:  Liya Wang; Hamid R Eghbalnia; Arash Bahrami; John L Markley
Journal:  J Biomol NMR       Date:  2005-05       Impact factor: 2.835

9.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
Journal:  Science       Date:  1993-07-16       Impact factor: 47.728

10.  Objective identification of residue ranges for the superposition of protein structures.

Authors:  Donata K Kirchner; Peter Güntert
Journal:  BMC Bioinformatics       Date:  2011-05-18       Impact factor: 3.169

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  16 in total

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2.  Systematic solution to homo-oligomeric structures determined by NMR.

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Journal:  Proteins       Date:  2015-02-05

3.  Protein structure prediction assisted with sparse NMR data in CASP13.

Authors:  Davide Sala; Yuanpeng Janet Huang; Casey A Cole; David A Snyder; Gaohua Liu; Yojiro Ishida; G V T Swapna; Kelly P Brock; Chris Sander; Krzysztof Fidelis; Andriy Kryshtafovych; Masayori Inouye; Roberto Tejero; Homayoun Valafar; Antonio Rosato; Gaetano T Montelione
Journal:  Proteins       Date:  2019-12

4.  Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Authors:  Julia Koehler Leman; Andrew R D'Avino; Yash Bhatnagar; Jeffrey J Gray
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5.  Core packing of well-defined X-ray and NMR structures is the same.

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6.  AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.

Authors:  Roberto Tejero; Yuanpeng Janet Huang; Theresa A Ramelot; Gaetano T Montelione
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7.  The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

Authors:  David A Snyder; Jennifer Grullon; Yuanpeng J Huang; Roberto Tejero; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

Review 8.  Computational approaches for inferring the functions of intrinsically disordered proteins.

Authors:  Mihaly Varadi; Wim Vranken; Mainak Guharoy; Peter Tompa
Journal:  Front Mol Biosci       Date:  2015-08-05

9.  Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.

Authors:  Fabien Mareuil; Thérèse E Malliavin; Michael Nilges; Benjamin Bardiaux
Journal:  J Biomol NMR       Date:  2015-04-11       Impact factor: 2.835

10.  Structure, Biosynthesis, and Biological Activity of Succinylated Forms of Bacteriocin BacSp222.

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Journal:  Int J Mol Sci       Date:  2021-06-10       Impact factor: 5.923

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