PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

Abstract

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

Quality assessment of protein NMR structures

“…In our opinion and experience, appropriate protocols for energy refinement, including the use of KB potentials and fragment libraries, can significantly improve the accuracy of NMR structures (see e.g., [1,3,20,21]), particularly for larger proteins determined with sparse restraint networks [4,5]. Approaches based on molecular dynamics can also often provide appreciable improvements in structure quality [22].…”

“…Table 1 provides a standard format used to report such restraint violations [9,20], although other formats are also common in the NMR literature. These metrics provide an overview of global (or average) restraint violation statistics, as well as information on the most significant outliers.…”

“…Clusters of restraint violations in regions of the 3D structure may indicate errors in the local structure. Methods have been described to convert between restraint formats [20,23,24], allowing initial restraint lists generated for one structure generation program to be used with alternative structure generation programs. The NOE completeness score [20,25] is a useful metric of structural accuracy, assessing the fraction of short distances in the model structure that are consistent with restraint data set.…”

“…Different regions of the structure are often converged to different degrees among conformers. In common practice, a distinction is made between well-defined and ill-defined (i.e., not-well-defined) regions [9,20]. In single-domain proteins, the backbone or all-heavy-atom root mean square deviation of coordinates (RMSD) computed after superposition of all the well-defined regions is taken as a measured of structure precision.…”

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

“…Unfortunately, efforts to develop universal restraint converters have been challenged because some restraint formats omit information required by other restraint formats 8 , and full parsing of each software-specific format has proven to be impossible. The current situation hampers the proper archiving and use of bio-molecular NMR data, and prevents the routine inclusion of NMR restraint validation in the wwPDB NMR validation pipeline.…”