SsPINE/ssPINE-POKY: Automated chemical shift assignment with an intuitive graphical user interface for solid-state NMR data from complex protein systems.

Abstract

In structural biology, nuclear magnetic resonance (NMR) is an important method when studying biological complexes with high resolution. Compared with solution NMR, solid-state NMR (ssNMR) has increased the possibility of studying large macromolecular assemblies with high structural complexity mainly related to low solubility. However, computational tools for the analysis of complex multidimensional ssNMR data have lagged behind those for solution NMR. Before a structure can be determined, thousands of signals from individual types of multidimensional ssNMR spectra of samples must be recognized, correlated, categorized, and eventually assigned to atoms in the chemical structure. To address these tedious steps, we have developed an automated algorithm for ssNMR spectra called “ssPINE”. The ssPINE software accepts the sequence of the protein plus peak lists from a variety of ssNMR experiments as inputs and offers automated backbone and side-chain assignments. To lower the bar of using ssPINE, we have developed a graphical user interface called ssPINE-POKY as a plugin to POKY that provides seamless communication between POKY and ssPINE webserver. The user only needs to select experiments in POKY to run a job and import results with just a few mouse clicks. Supported by NSF DBI-2051595, DBI-1902076 and University of Colorado Denver.