Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2013 Feb 15;29(4):515-7. doi: 10.1093/bioinformatics/bts692. Epub 2012 Dec 7.

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy.

Author information

1
National Magnetics Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA. whlee@nmrfam.wisc.edu

Abstract

SUMMARY:

ADAPT-nuclear magnetic resonance (ADAPT-NMR) offers an automated approach to the concurrent acquisition and processing of protein NMR data with the goal of complete backbone and side chain assignments. What the approach lacks is a useful graphical interface for reviewing results and for searching for missing peaks that may have prevented assignments or led to incorrect assignments. Because most of the data ADAPT-NMR collects are 2D tilted planes used to find peaks in 3D spectra, it would be helpful to have a tool that reconstructs the 3D spectra. The software package reported here, ADAPT-NMR Enhancer, supports the visualization of both 2D tilted planes and reconstructed 3D peaks on each tilted plane. ADAPT-NMR Enhancer can be used interactively with ADAPT-NMR to automatically assign selected peaks, or it can be used to produce PINE-SPARKY-like graphical dialogs that support atom-by-atom and peak-by-peak assignment strategies. Results can be exported in various formats, including XEASY proton file (.prot), PINE pre-assignment file (.str), PINE probabilistic output file, SPARKY peak list file (.list) and TALOS+ input file (.tab). As an example, we show how ADAPT-NMR Enhancer was used to extend the automated data collection and assignment results for the protein Aedes aegypti sterol carrier protein 2.

AVAILABILITY:

The program, in the form of binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/adapt-nmr-enhancer.

PMID:
23220573
PMCID:
PMC3570218
DOI:
10.1093/bioinformatics/bts692
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center