Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm

J Biomol NMR. 2008 Aug;41(4):221-39. doi: 10.1007/s10858-008-9255-1. Epub 2008 Jul 31.


We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms*
  • Animals
  • Bacterial Proteins / chemistry
  • Carrier Proteins / chemistry
  • DNA-Binding Proteins / chemistry
  • Efficiency
  • Escherichia coli Proteins / chemistry
  • Humans
  • Interleukin-4 / chemistry
  • Likelihood Functions
  • Methanobacterium / chemistry
  • Mice
  • Models, Chemical
  • Models, Molecular
  • Nitrite Reductases / chemistry
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Pattern Recognition, Automated / methods
  • Protein Conformation*
  • Research Design
  • Signal Processing, Computer-Assisted*
  • Thiamin-Triphosphatase / chemistry


  • Bacterial Proteins
  • Carrier Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • IL4 protein, human
  • YmoA protein, Yersinia enterocolitica
  • cyanovirin N
  • Interleukin-4
  • Nitrite Reductases
  • Thiamin-Triphosphatase