An overview of tools for the validation of protein NMR structures
| Autor: | Jurgen F. Doreleijers, Pieter M. S. Hendrickx, Aleksandras Gutmanas, Geerten W. Vuister, Rasmus H. Fogh |
|---|---|
| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Protein Conformation Chemistry Protein Data Bank (RCSB PDB) Proteins Reproducibility of Results Computational biology Nuclear magnetic resonance spectroscopy Biochemistry Crystallography Protein structure Atomic resolution Databases Protein Nuclear Magnetic Resonance Biomolecular Software Spectroscopy Staphylococcal Nuclease |
| Zdroj: | Journal of Biomolecular NMR ICT FP7 Publications Database OpenAIRE |
| ISSN: | 1573-5001 0925-2738 |
| DOI: | 10.1007/s10858-013-9750-x |
| Popis: | Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11 % of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9). |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink