PINE-SPARKY

[…] conformational changes, internal dynamics and protein–ligand interactions. as a means for facilitating the handling and analysis of spectra involved in these types of nmr studies, we have developed pine-sparky.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. the graphical user interface of pine-sparky.2 […]

[…] for rdc measurements., signals for sequence-specific backbone resonance assignments were detected by apes [] and assigned by pine algorithm [], and followed with subsequent manual verification by pine-sparky []. due to tev cleavage site introduced into purification constructs, gefgs is present at the n-terminus, followed by the methionine at position 1 of the native ydj1 protein sequence. […]

[…] go. all collected spectra were processed and analyzed via xwin nmr (bruker instruments, karlsruhe, germany), nmrpipe/nmrdraw (biosym/molecular simulation, inc. san diego, ca, usa) software, and the pine-sparky program., circular dichroism (cd) spectroscopic studies– were performed using a j-815 spectrophotometer (jasco, japan) equipped with a peltier system for controlling the temperature. […]

[…] , 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 […]

[…] 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 […]