NDLI: An artificial backbone of hydrogens for finding the conformation of protein molecules

Content Provider	IEEE Xplore Digital Library
Author	Lavor, C. Mucherino, A. Liberti, L. Maculan, N.
Copyright Year	2009
Description	Author affiliation: Dept. of Applied Mathematics (IMECC-UNICAMP), State University of Campinas, Campinas-SP, Brazil (Lavor, C.; Mucherino, A.; Liberti, L.; Maculan, N.)
Abstract	NMR experiments can provide distances between pairs of hydrogens of a protein molecule. The problem of identifying the coordinates of such hydrogens by exploiting the information on the distances is a Molecular Distance Geometry Problem (MDGP). In a previous work, we defined an artificial backbone of hydrogens related to the protein backbones, where a particular ordering was given to the hydrogens. This ordering allows to formulate the MDGP as a combinatorial optimization problem, to which we refer as the Discretizable MDGP (DMDGP) and that we efficiently solve by an exact algorithm, the Branch and Prune (BP) algorithm. Once the coordinates of the hydrogens have been found, the problem of finding the remaining backbone atoms (N, C and C) is another MDGP. In this short paper, we propose a simple method for solving the MDGP related to the backbone atoms N, C and C of a protein, where the coordinates of the hydrogens previously found by the BP algorithm are exploited.
Starting Page	152
Ending Page	155
File Size	266693
Page Count	4
File Format	PDF
ISBN	9781424451210
DOI	10.1109/BIBMW.2009.5332119
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-11-01
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Protein engineering Information geometry NP-hard problem Spine Hydrogen Optimization methods Systems engineering and theory Digital arithmetic Mathematics Nuclear magnetic resonance
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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