ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy
Autor(es): Lee, Woonghee; Bahrami, Arash; Markley, John L.
Resumo: 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.Contact: whlee[at]nmrfam.wisc.edu or markley[at]nmrfam.wisc.edu
Palavras-Chave: Computer programs; Resonance; Analytical techniques; Proteins; Aquatic insects; Magnetic resonance spectroscopy; Computer graphics; N.M.R.; Bioinformatics
Imprenta: Bioinformatics, v. 29, n. 4, p. 515-517, 2013.
Descritores: Aedes aegypti - Proteins
Data de publicação: 2013
