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Protocols

SPARTA+ specifications

Information


Unique identifier OMICS_05515
Name SPARTA+
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yang Shen

Information


Unique identifier OMICS_05515
Name SPARTA+
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Shen

Publication for SPARTA+

SPARTA+ citations

 (13)
library_books

The PROSECCO server for chemical shift predictions in ordered and disordered proteins

2017
J Biomol NMR
PMCID: 5711976
PMID: 29119515
DOI: 10.1007/s10858-017-0145-2

[…] n accurate method to individuate secondary structure elements from protein chemical shifts. Additional entries to the parameterizing dataset were employed exclusively for benchmarking PROSECCOFOLDED, SPARTA+ (Shen and Bax ) and CamShift (Kohlhoff et al. ). In particular, the selected benchmark database contained 77 BMRB entries having all been deposited after 2016, which ensured that these data we […]

library_books

Biophysical characterization of the calmodulin like domain of Plasmodium falciparum calcium dependent protein kinase 3

2017
PLoS One
PMCID: 5528832
PMID: 28746405
DOI: 10.1371/journal.pone.0181721

[…] clustered using 3 Å cutoff using Rosetta’s clustering application and the lowest energy model with a chemical shift root-mean-squared difference between experimental and chemical shifts predicted by SPARTA+ [] better than one standard deviation from the ensemble mean was selected as the structural representative. The generated structures were used in hydrodynamic calculations of correlational tim […]

library_books

Fe65 PTB2 Dimerization Mimics Fe65 APP Interaction

2017
PMCID: 5425604
PMID: 28553201
DOI: 10.3389/fnmol.2017.00140

[…] nd CBCA(CO)NH spectra of the C633E mutant. Chemical shift based secondary structure predictions and structure based chemical shift predictions where done using the programs TALOS+ (Shen et al., ) and SPARTA+ (Shen and Bax, ). Model-free Liparai-Szabo parameters derived from the 15N relaxation data of the C633E mutant were analyzed and compared to hydrodynamic diffusion tensors using the programs R […]

library_books

Cataract associated P23T γD crystallin retains a native like fold in amorphous looking aggregates formed at physiological pH

2017
Nat Commun
PMCID: 5424181
PMID: 28474685
DOI: 10.1038/ncomms15137

[…] rnatively, a hypothetical completely parallel β-sheet structure of P23T hγD was built using the PyMOL Molecular Graphics System (Schrödinger, LLC), from which chemical shifts were predicted using the SPARTA+ program. Subsequently, synthetic 2D NMR spectra showing the predicted one-bond cross-peaks were generated using utilities from the NMRPipe software package. The solution NMR peak markers in w […]

call_split

Protein structure refinement using a quantum mechanics based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

2016
PMCID: 5399634
PMID: 28451325
DOI: 10.1039/c6sc04344e
call_split See protocol

[…] e ensemble using hierarchical agglomerative clustering.CheShift-2 () calculations were performed with the CheShift-2 PyMOL-plugin found at ; http://github.com/aloctavodia/cheshift. CamShift, PPM One, Sparta+, shAIC, and ShiftX2 () calculations are performed using the stand-alone predictors. Scripts to automate these predictions can be found at ; http://github.com/larsbratholm/cs_prediction.Much of […]

library_books

Chemical shift guided homology modeling of larger proteins

2015
Nat Methods
PMCID: 4521993
PMID: 26053889
DOI: 10.1038/nmeth.3437

[…] the same method developed for the standard CS-Rosetta protocol. Specifically, for each all-atom model, a χ2 value is first calculated between the experimental chemical shifts and values predicted by SPARTA+ , which is then added to the Rosetta all-atom energy. This chemical shift re-scored Rosetta all-atom energy is used to evaluate and select the final models. […]

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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