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Showing results for xplor
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Xplor-NIH for molecular structure determination from NMR and other data sources.
Schwieters CD, Bermejo GA, Clore GM. Schwieters CD, et al. Protein Sci. 2018 Jan;27(1):26-40. doi: 10.1002/pro.3248. Epub 2017 Sep 18. Protein Sci. 2018. PMID: 28766807 Free PMC article.
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. ...Finally, the different available force fields are presented, among other Xplor-NIH capabilities....
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data …
Xplor-NIH: Better parameters and protocols for NMR protein structure determination.
Bermejo GA, Tjandra N, Clore GM, Schwieters CD. Bermejo GA, et al. Protein Sci. 2024 Apr;33(4):e4922. doi: 10.1002/pro.4922. Protein Sci. 2024. PMID: 38501482
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, s …
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular struc …
Using small angle solution scattering data in Xplor-NIH structure calculations.
Schwieters CD, Clore GM. Schwieters CD, et al. Prog Nucl Magn Reson Spectrosc. 2014 Jul;80:1-11. doi: 10.1016/j.pnmrs.2014.03.001. Epub 2014 Apr 3. Prog Nucl Magn Reson Spectrosc. 2014. PMID: 24924264 Free PMC article. Review.
This contribution describes the use of small and wide angle X-ray and small angle neutron scattering for biomolecular structure calculation using the program Xplor-NIH, both with and without NMR data. The current algorithms used for calculating scattering curves are descri …
This contribution describes the use of small and wide angle X-ray and small angle neutron scattering for biomolecular structure calculation …
The Xplor-NIH NMR molecular structure determination package.
Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM. Schwieters CD, et al. J Magn Reson. 2003 Jan;160(1):65-73. doi: 10.1016/s1090-7807(02)00014-9. J Magn Reson. 2003. PMID: 12565051
We announce the availability of the Xplor-NIH software package for NMR biomolecular structure determination. This package consists of the pre-existing XPLOR program, along with many NMR-specific extensions developed at the NIH. ...
We announce the availability of the Xplor-NIH software package for NMR biomolecular structure determination. This package consists of …
Xplor 2--an optimized transformation/expression system for recombinant protein production in the yeast Arxula adeninivorans.
Böer E, Piontek M, Kunze G. Böer E, et al. Appl Microbiol Biotechnol. 2009 Sep;84(3):583-94. doi: 10.1007/s00253-009-2167-5. Epub 2009 Aug 12. Appl Microbiol Biotechnol. 2009. PMID: 19672589
Based on a redesign of the basic vector, a new Arxula vector system, Xplor 2, for heterologous gene expression was established, which allows (1) the construction of expression plasmids for supertransformation of A. adeninivorans strains secreting target proteins of biotech …
Based on a redesign of the basic vector, a new Arxula vector system, Xplor 2, for heterologous gene expression was established, which …
Paramagnetism-based restraints for Xplor-NIH.
Banci L, Bertini I, Cavallaro G, Giachetti A, Luchinat C, Parigi G. Banci L, et al. J Biomol NMR. 2004 Mar;28(3):249-61. doi: 10.1023/B:JNMR.0000013703.30623.f7. J Biomol NMR. 2004. PMID: 14752258
Modules that use paramagnetism-based NMR restraints have been developed and integrated in the well known program for solution structure determination Xplor-NIH; the complete set of such modules is called PARArestraints for Xplor-NIH. ...Furthermore, the same experim …
Modules that use paramagnetism-based NMR restraints have been developed and integrated in the well known program for solution structure dete …
Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.
Bermejo GA, Schwieters CD. Bermejo GA, et al. Methods Mol Biol. 2018;1688:311-340. doi: 10.1007/978-1-4939-7386-6_14. Methods Mol Biol. 2018. PMID: 29151215 Free PMC article.
Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter illustrates its use with the de novo structure determination of the B1 domain of streptococcal protein G (GB1), based on distances from nuc …
Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter …
A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination.
Schwieters CD, Bermejo GA, Clore GM. Schwieters CD, et al. Protein Sci. 2020 Jan;29(1):100-110. doi: 10.1002/pro.3745. Epub 2019 Oct 27. Protein Sci. 2020. PMID: 31613020 Free PMC article.
We introduce a new hydrogen bonding potential of mean force generated from high-quality crystal structures for use in Xplor-NIH structure calculations. This term applies to hydrogen bonds involving both backbone and sidechain atoms. When used in structure refinement calcul …
We introduce a new hydrogen bonding potential of mean force generated from high-quality crystal structures for use in Xplor-NIH struc …
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.
Tian Y, Schwieters CD, Opella SJ, Marassi FM. Tian Y, et al. J Biomol NMR. 2017 Jan;67(1):35-49. doi: 10.1007/s10858-016-0082-5. Epub 2016 Dec 29. J Biomol NMR. 2017. PMID: 28035651 Free PMC article.
Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM …
Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrost …
The VMD-XPLOR visualization package for NMR structure refinement.
Schwieters CD, Clore GM. Schwieters CD, et al. J Magn Reson. 2001 Apr;149(2):239-44. doi: 10.1006/jmre.2001.2300. J Magn Reson. 2001. PMID: 11318623
In this paper we present the VMD-XPLOR package combining the XPLOR refinement program and the VMD visualization program and including extensions for use in the determination of biomolecular structures from NMR data. ...Finally, the VMD-XPLOR interface is modu …
In this paper we present the VMD-XPLOR package combining the XPLOR refinement program and the VMD visualization program and in …
286 results