Literature DB >> 28766807

Xplor-NIH for molecular structure determination from NMR and other data sources.

Charles D Schwieters1, Guillermo A Bermejo1, G Marius Clore2.   

Abstract

Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects. Finally, the different available force fields are presented, among other Xplor-NIH capabilities.
© 2017 This article is a U.S. Government work and is in the public domain in the USA.

Keywords:  NMR restraints; SAXS; computational toolbox; cryo-electron microscopy; nucleic acid; optimization; protein; structure determination

Mesh：

Year:  2017        PMID： 28766807      PMCID： PMC5734396          DOI： 10.1002/pro.3248

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  58 in total

1.  Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.

Authors:  J Kuszewski; C Schwieters; G M Clore
Journal:  J Am Chem Soc       Date:  2001-05-02       Impact factor: 15.419

2.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

3.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.

Authors:  Alexander W Schüttelkopf; Daan M F van Aalten
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-07-21

4.  Efficient modeling of symmetric protein aggregates from NMR data.

Authors:  Benjamin Bardiaux; Barth-Jan van Rossum; Michael Nilges; Hartmut Oschkinat
Journal:  Angew Chem Int Ed Engl       Date:  2012-05-31       Impact factor: 15.336

5.  Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structures.

Authors:  Wolfgang Rieping; Michael Habeck; Michael Nilges
Journal:  J Am Chem Soc       Date:  2005-11-23       Impact factor: 15.419

6.  A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data.

Authors:  Charles D Schwieters; G Marius Clore
Journal:  J Phys Chem B       Date:  2007-12-19       Impact factor: 2.991

7.  Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR.

Authors:  S K Straus; W R P Scott; C D Schwieters; D A Marvin
Journal:  Eur Biophys J       Date:  2010-11-17       Impact factor: 1.733

8.  High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

Authors:  Ye Tian; Charles D Schwieters; Stanley J Opella; Francesca M Marassi
Journal:  J Biomol NMR       Date:  2016-12-29       Impact factor: 2.835

9.  Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes.

Authors:  Yaroslav Ryabov; Jeong-Yong Suh; Alexander Grishaev; G Marius Clore; Charles D Schwieters
Journal:  J Am Chem Soc       Date:  2009-07-15       Impact factor: 15.419

10.  Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry.

Authors:  Rebecca S Lipsitz; Yugal Sharma; Bernard R Brooks; Nico Tjandra
Journal:  J Am Chem Soc       Date:  2002-09-04       Impact factor: 15.419
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  65 in total

1.  Probing initial transient oligomerization events facilitating Huntingtin fibril nucleation at atomic resolution by relaxation-based NMR.

Authors:  Samuel A Kotler; Vitali Tugarinov; Thomas Schmidt; Alberto Ceccon; David S Libich; Rodolfo Ghirlando; Charles D Schwieters; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-11       Impact factor: 11.205

2.  Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Authors:  Brinda Vallat; Benjamin Webb; John D Westbrook; Andrej Sali; Helen M Berman
Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

3.  Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.

Authors:  Zhou Gong; Charles D Schwieters; Chun Tang
Journal:  Methods       Date:  2018-04-12       Impact factor: 3.608

4.  Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly.

Authors:  Shibani Bhattacharya; Christopher B Stanley; William T Heller; Peter A Friedman; Zimei Bu
Journal:  J Biol Chem       Date:  2019-06-06       Impact factor: 5.157

5.  Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins.

Authors:  Liang Qin; Fredj Ben Bdira; Yann G J Sterckx; Alexander N Volkov; Jocelyne Vreede; Gabriele Giachin; Peter van Schaik; Marcellus Ubbink; Remus T Dame
Journal:  Nucleic Acids Res       Date:  2020-02-28       Impact factor: 16.971

Review 6.  Principles for Integrative Structural Biology Studies.

Authors:  Michael P Rout; Andrej Sali
Journal:  Cell       Date:  2019-05-30       Impact factor: 41.582

7.  Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif.

Authors:  Jin Wen; Hui Liao; Kye Stachowski; Jordan P Hempfling; Ziqing Qian; Chunhua Yuan; Mark P Foster; Dehua Pei
Journal:  Bioorg Med Chem       Date:  2020-08-18       Impact factor: 3.641

8.  Interaction of Huntingtin Exon-1 Peptides with Lipid-Based Micellar Nanoparticles Probed by Solution NMR and Q-Band Pulsed EPR.

Authors:  Alberto Ceccon; Thomas Schmidt; Vitali Tugarinov; Samuel A Kotler; Charles D Schwieters; G Marius Clore
Journal:  J Am Chem Soc       Date:  2018-05-14       Impact factor: 15.419

9.  Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions.

Authors:  Yusuke Okuno; Attila Szabo; G Marius Clore
Journal:  J Am Chem Soc       Date:  2020-04-24       Impact factor: 15.419

10.  Contributions of different modules of the plasminogen-binding Streptococcus pyogenes M-protein that mediate its functional dimerization.

Authors:  Cunjia Qiu; Yue Yuan; Jaroslav Zajicek; Zhong Liang; Rashna D Balsara; Teresa Brito-Robionson; Shaun W Lee; Victoria A Ploplis; Francis J Castellino
Journal:  J Struct Biol       Date:  2018-07-30       Impact factor: 2.867
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