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Author, Editor(s)

Author(s):

Dietzen, Matthias
Zotenko, Elena
Hildebrandt, Andreas
Lengauer, Thomas

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Not MPG Author(s):

Hildebrandt, Andreas

BibTeX cite key*:

Dietzen2012

Title

Title*:

On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking

Journal

Journal Title*:

Journal of Chemical Information and Modeling

Journal's URL:


Download URL
for the article:

http://pubs.acs.org/doi/abs/10.1021/ci2004847

Language:

English

Publisher

Publisher's
Name:

American Chemical Society

Publisher's URL:


Publisher's
Address:

Washington, DC

ISSN:

1549-9596

Vol, No, pp, Date

Volume*:

52

Number:

3

Publishing Date:

February 2012

Pages*:

844-856

Number of
VG Pages:


Page Start:

844

Page End:

856

Sequence Number:


DOI:

10.1021/ci2004847

Note, Abstract, ©

Note:


(LaTeX) Abstract:

Incorporating backbone flexibility into protein–ligand docking is still a challenging problem. In protein–protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein–ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its Cα trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.

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Access Level:

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Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

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BibTeX Entry:

@ARTICLE{Dietzen2012,
AUTHOR = {Dietzen, Matthias and Zotenko, Elena and Hildebrandt, Andreas and Lengauer, Thomas},
TITLE = {On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking},
JOURNAL = {Journal of Chemical Information and Modeling},
PUBLISHER = {American Chemical Society},
YEAR = {2012},
NUMBER = {3},
VOLUME = {52},
PAGES = {844--856},
ADDRESS = {Washington, DC},
MONTH = {February},
ISBN = {1549-9596},
DOI = {10.1021/ci2004847},
}


Entry last modified by Anja Becker, 02/12/2013
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Editor(s)
[Library]
Created
12/13/2012 03:03:53 PM
Revisions
5.
4.
3.
2.
1.
Editor(s)
Anja Becker
Ruth Schneppen-Christmann
Manuel Lamotte-Schubert
Matthias Dietzen
Matthias Dietzen
Edit Dates
12.02.2013 13:12:35
10.01.2013 11:27:44
21.12.2012 08:38:19
13.12.2012 15:07:03
13.12.2012 15:04:55