The Xplor-NIH NMR molecular structure determination package.

By C. Schwieters, J. Kuszewski, N. Tjandra, G. Clore. 2003

2,250 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Santrupti Nerli
2. Nikolaos G. Sgourakis
3. Woonghee Lee
4. John L. Markley
5. Alexandre M. J. J. Bonvin
6. Gaetano T. Montelione
7. Andrew C. McShan
8. Debora Marks

In Molecular Biology

1. Santrupti Nerli
2. Nikolaos G. Sgourakis
3. Alexandre M. J. J. Bonvin
4. Debora Marks
5. Woonghee Lee
6. Andrew C. McShan
7. John L. Markley
8. Christopher Sander

Citations in the corpus

• The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data (2016, methodology): “C/S offers two options in ‘‘constraints only for the final step’’: (1) the traditional method of explicit water refinement followed by simulated annealing, and (2) concurrent implicit water solvation with EEFx (Effective Energy Function for Xplor - NIH ) potential during simulated annealing (Tian et a”
• Version 1.2 of the Crystallography and NMR system (2007, methodology): “Examples of such interfaces include tools developed for NMR structure determinatio”
• Structural Basis for Sequence Specific DNA Binding and Protein Dimerization of HOXA13 (2011, methodology): “Structure calculations were performed using the YASAP protocol within X-PLOR [48,49], as described previously [50].”
• 3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “, 2009), a coarse-grained modeler that uses a combination secondary structure and tertiary contacts as inputs, followed by refinement in XPLOR (Schwieters et al., 2003).”
• ACPYPE - AnteChamber PYthon Parser interfacE (2012, background): “CNS and XPLOR (including its variant XPLOR-NIH [6] [7]) have a function called LEARn that only generates parameter information, no topology nor charges.”
• PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination (2014, methodology): “Ponderosa Server generates water bath and smooth torsion angle potential refinement scripts (Bermejo et al. 2012) and executes them via XPLOR-NIH (Schwieters et al. 2003) to generate energetically favorable structures.”
• Evaluating protein structures determined by structural genomics consortia (2006, methodology): “Some structures refined using XPLOR (both the original 31 and the NIH version 53 ) also have high scores for these two parameters.”
• Chemical shift-based methods in NMR structure determination (2018, methodology): “Year Description (method) Reference 1993 NOE assignment and structure refinement approach (ASNO) [213] 1995 Introduction of ambiguous NOE distance restraints [144] 1997 Protein structure determination methods using fragment assembly (Ab initio) [57,58] 1997 NMR structure calculation using ambiguous ”