PINE-SPARKY

[…] PINE-SPARKY.2 can be launched from the automated assignment sub-menu of NMRFAM menu or by typing the two-letter-code ep in the NMRFAM-SPARKY. This opens a graphical user interface that makes all the f […]

[…] .org/en/nmr_tool_box/magro_nmrview.html) , with NMRView and CcpNmr (http://www.ccpn.ac.uk/). Programs for automated assignment of backbone and side chain signals are also available, such as PINE and PINE-SPARKY, which is included in the new version of Sparky (NMRFAM-Sparky) , , MARS , UNIO (assembly of MATCH/ASCAN/CANDID/ATNOS algorithms) , , , , and FLYA , which is partially powered by the GARA […]

[…] s are accompanied by efficient visual verification tools: automated peak picking can be verified by a tool in NMRFAM-SPARKY; errors in automated assignments by PINE can be detected and corrected with PINE-SPARKY (Lee et al. ) or ARECA (Dashti et al. ); and errors in automated structure calculations can be detected and corrected by the visual tools that are part of Ponderosa Analyzer.A goal of Inte […]

[…] iated with particular NMR experiments.Fig. 4ADAPT-NMR Enhancer and ARECA can be used to validate the chemical shift assignments generated by ADAPT-NMR. Validation of PINE’s output can be performed by PINE-SPARKY (Lee et al. ) (incorporated into NMRFAM-SPARKY), or the ARECA package. […]

[…] ases, the temperature was maintained at 30 °C. 2D 1H{15N} HSQC, 3D HNCA, 3D HN(CA)CO, 3D HNCO, 3D HNCACB, and 3D CBCA(CO)NH peak lists for NP4 were used as input to the PINE server and, employing the PINE-SPARKY extension, were used to determine sequence-specific backbone resonance assignments. Assignment data were collected at pH 7.3 for NP4, referenced to DSS, and are listed in Table S1 of the . […]

[…] e, by stepwise judicious selection of cloning vector (pE-SUMO), host strain, isolation and purification protocols, the C105A mutation, and solution conditions. Linkage of the output from PINE-NMR to PINE-SPARKY validations facilitated and virtually automated the spectral peak assignments. The final structure was of high quality and well supported by the extensive datasets. […]