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Bioinformatics Advance Access published online on September 23, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti043
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 11, 2004
Revised September 2, 2004
Accepted September 19, 2004

Applications note

APART: automated pre-processing for NMR assignments with reduced tedium

Norma H. Pawley 1, Jason D. Gans 1, and Ryszard Michalczyk 1*

1 Los Alamos National Laboratory, Bioscience Division, MS G758, Los Alamos, New Mexico 87545

* To whom correspondence should be addressed. E-mail: rmichalczyk{at}lanl.gov.


  Abstract

Motivation: High-throughput NMR structure determination is a goal that will require progress on many fronts, one of which is rapid resonance assignment. An important rate-limiting step in the resonance assignment process is accurate identification of resonance peaks in NMR spectra. Peak-picking schemes range from incomplete (which lose essential assignment connectivities) to noisy (which obscure true connectivities with many false ones). We introduce an automated pre-assignment process that removes false peaks from noisy peak lists by requiring consensus between multiple NMR experiments and exploiting a priori information about NMR spectra. This process is designed to accept multiple input formats and generate multiple output formats, in an effort to be compatible with a variety of user preferences.

Results: Automated pre-processing with APART rapidly identifies and removes false peaks from initial peak lists, reduces the burden of manual data entry, and documents and standardizes the peak filtering process. Successful pre-processing is demonstrated by the increased number of correct assignments obtained when data is submitted to an automated assignment program.

Availability: APART is available from http://sir.lanl.gov/NMR/APART.htm.

Supplementary Information: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APART_Manual.pdf.


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