A topology-constrained distance network algorithm for protein structure determination from NOESY data

Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality of input data and final 3D structures is evaluated using recall, precision, and F-measure (RPF) scores, a statistical measure of goodness of fit with the input data. AutoStructure has been tested on three protein NMR data sets for which high-quality structures have previously been solved by an expert, and yields comparable high-quality distance constraint lists and 3D protein structures in hours. We also compare several protein structures determined using AutoStructure with corresponding homologous proteins determined with other independent methods. The program has been used in more than two dozen protein structure determinations, several of which have already been published.

Original languageEnglish (US)
Pages (from-to)587-603
Number of pages17
JournalProteins: Structure, Function and Genetics
Volume62
Issue number3
DOIs
StatePublished - Feb 15 2006

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Spectrum Analysis
Topology
Spectroscopy
Proteins
Electric network analysis
Graph theory
Amino Acid Sequence
Software
Nuclear magnetic resonance
Amino Acids
Experiments

Keywords

  • AutoStructure
  • Automated NMR structure determination
  • Constraint network analysis
  • Fold topology constraints
  • Graph theory
  • RPF

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

A topology-constrained distance network algorithm for protein structure determination from NOESY data. / Huang, Yuanpeng Janet; Tejero, Roberto; Powers, Robert; Montelione, Gaetano T.

In: Proteins: Structure, Function and Genetics, Vol. 62, No. 3, 15.02.2006, p. 587-603.

Research output: Contribution to journalArticle

Huang, Yuanpeng Janet ; Tejero, Roberto ; Powers, Robert ; Montelione, Gaetano T. / A topology-constrained distance network algorithm for protein structure determination from NOESY data. In: Proteins: Structure, Function and Genetics. 2006 ; Vol. 62, No. 3. pp. 587-603.
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