Journal of Biomolecular NMR

, Volume 56, Issue 4, pp 337–351 | Cite as

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

  • Roberto Tejero
  • David Snyder
  • Binchen Mao
  • James M. Aramini
  • Gaetano T. Montelione
Article

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.

Keywords

Protein NMR structure validation BioMagResDatabase XPLOR CNS CYANA CS-Rosetta 

Abbreviations

ACO

Dihedral angle constraint

CNSw

Protocol using the crystallography and NMR software (CNS) package for restrained structure refinement in explicit water solvent

DAOP

Dihedral angle order parameter

CS

Chemical shift

rCS-Rosetta

Restrained chemical shift-directed Rosetta

RDC

Residual dipolar coupling

SVD

Singular value decomposition

RMSD

Root mean squared deviation

Supplementary material

10858_2013_9753_MOESM1_ESM.pdf (248 kb)
Supplementary material 1 (PDF 247 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Roberto Tejero
    • 1
    • 2
    • 3
    • 4
  • David Snyder
    • 5
  • Binchen Mao
    • 1
    • 2
    • 3
  • James M. Aramini
    • 1
    • 2
    • 3
  • Gaetano T. Montelione
    • 1
    • 2
    • 3
  1. 1.Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayUSA
  2. 2.Robert Wood Johnson Medical SchoolRutgers, The State University of New JerseyPiscatawayUSA
  3. 3.Northeast Structural Genomics ConsortiumPiscatawayUSA
  4. 4.Departamento de Quίmica FίsicaUniversidad de ValenciaBurjassot, ValenciaSpain
  5. 5.Department of ChemistryWilliam Paterson UniversityWayneUSA

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