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SPARTA specifications

Information


Unique identifier OMICS_05514
Name SPARTA
Alternative name Shifts Predicted from Analogy in Residue type and Torsion Angle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yang Shen

Publication for Shifts Predicted from Analogy in Residue type and Torsion Angle

SPARTA citations

 (7)
call_split

Solution structure of the isolated histone H2A H2B heterodimer

2016
Sci Rep
PMCID: 4867618
PMID: 27181506
DOI: 10.1038/srep24999
call_split See protocol

[…] The solution structures of the isolated H2A-H2B heterodimer were modeled by the CS-Rosetta program, which is a combination of the Rosetta program, the SPARTA program and MFR scripts and is able to generate model structures consistent with the observed chemical shifts. To obtain the overall structure of H2A-H2B, first the structure of the core region […]

library_books

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

2016
J Biomol NMR
PMCID: 4921114
PMID: 27169728
DOI: 10.1007/s10858-016-0036-y

[…] e growing number and variety of protein structures deposited in the Protein Data Bank (PDB) to assist in determining protein structures from NMR data. Shen and Bax () introduced a method that employs SPARTA to refine fragment libraries used as input to Rosetta structure calculations (Shen et al. ). The CS-HM-Rosetta using 4D data has extended this approach to larger proteins (Thompson et al. ). Th […]

library_books

The Cold Shock Domain of YB 1 Segregates RNA from DNA by Non Bonded Interactions

2015
PLoS One
PMCID: 4493011
PMID: 26147853
DOI: 10.1371/journal.pone.0130318

[…] To validate the trajectories, the NMR data available at BioMagResBank (entry number 4147 []) were used. The comparison between experimental and calculated chemical shifts was achieved with Sparta software [] using Cα- and Cβ-atoms (). The stereochemical parameters of the models at the different steps of the trajectories were also examined with the Procheck packages []. An example of Ram […]

library_books

Bayesian inference of protein structure from chemical shift data

2015
PeerJ
PMCID: 4375973
PMID: 25825683
DOI: 10.7717/peerj.861

[…] cessfully refined slightly denatured protein structures to a Cα-RMSD of down to 0.84 Å from the corresponding crystal structures (). The groups of Bax and Baker added the chi-square agreement between SPARTA () predicted chemical shift values and experimental chemical shifts with an empirical weight of 0.25 to the ROSETTA all-atom energy (; ). The ProCS method () uses an approach similar to that of […]

library_books

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

2013
PLoS One
PMCID: 3877219
PMID: 24391900
DOI: 10.1371/journal.pone.0084123

[…] e structural information that is being used increasingly in the determination of protein structure and dynamics. This is made possible primarily by empirical chemical shift predictors such as SHIFTS, SPARTA, SHIFTX, PROSHIFT, and CamShift –. While these methods generally offer quite accurate predictions, the predicted chemical shifts of backbone amide protons () tend to be significantly less accur […]

library_books

A software framework for analysing solid state MAS NMR data

2011
J Biomol NMR
PMCID: 3222832
PMID: 21953355
DOI: 10.1007/s10858-011-9569-2

[…] bility of CcpNmr Analysis to create synthetic peak lists. One possibility, for instance, is to import chemical shift lists from the BMRB or shift prediction programs such as SHIFTX (Neal et al. ) and SPARTA (Shen and Bax ) using the CcpNmr Format Converter. These shift lists can then be used to create peaks for any type of spectrum with any type of isotopic labelling in order to compare predicted […]

Citations

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SPARTA institution(s)
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA

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