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Author, Editor(s)

Author(s):

Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas

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BibTeX cite key*:

Steffen2006a

Title

Title*:

Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm

Journal

Journal Title*:

Journal of Chemical Information and Modeling

Journal's URL:

http://pubs.acs.org/journals/jcisd8/index.html

Download URL
for the article:

http://pubs.acs.org/cgi-bin/article.cgi/jcisd8/2006/46/i04/pdf/ci060072v.pdf

Language:

English

Publisher

Publisher's
Name:

American Chemical Society

Publisher's URL:

http://pubs.acs.org/

Publisher's
Address:

Washington DC, USA

ISSN:

1549-9596

Vol, No, pp, Date

Volume*:

46

Number:

4

Publishing Date:

July 2006

Pages*:

1695-1703

Number of
VG Pages:

9

Page Start:

1695

Page End:

1703

Sequence Number:


DOI:


Note, Abstract, ©

Note:


(LaTeX) Abstract:

We present a new algorithm for the fast and reliable structure prediction of synthetic receptor-ligand complexes. Our method is based on the protein-ligand docking program FlexX and extends our recently introduced docking technique for synthetic receptors, which has been implemented in the program FlexR. To handle the flexibility of the relevant molecules, we apply a novel docking strategy that uses an adaptive two-sided incremental construction algorithm which incorporates the structural flexibility of both the ligand and synthetic receptor. We follow an adaptive strategy, in which one molecule is expanded by attaching its next fragment in all possible torsion angles, whereas the other (partially assembled) molecule serves as a rigid binding partner. Then the roles of the molecules are exchanged. Geometric filters are used to discard partial conformations that cannot realize a targeted interaction pattern derived in a graph-based precomputation phase. The process is repeated until the entire complex is built up. Our algorithm produces promising results on a test data set comprising 10 complexes of synthetic receptors and ligands. The method generated near-native solutions compared to crystal structures in all but one case. It is able to generate solutions within a couple of minutes and has the potential of being used as a virtual screening tool for searching for suitable guest molecules for a given synthetic receptor in large databases of guests and vice versa.

URL for the Abstract:

http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2006/46/i04/abs/ci060072v.html

Categories,
Keywords:


HyperLinks / References / URLs:


Copyright Message:

Copyright 2006 American Chemical Society.

Personal Comments:


Download
Access Level:

Intranet

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort


BibTeX Entry:

@ARTICLE{Steffen2006a,
AUTHOR = {Steffen, Andreas and K{\"a}mper, Andreas and Lengauer, Thomas},
TITLE = {Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm},
JOURNAL = {Journal of Chemical Information and Modeling},
PUBLISHER = {American Chemical Society},
YEAR = {2006},
NUMBER = {4},
VOLUME = {46},
PAGES = {1695--1703},
ADDRESS = {Washington DC, USA},
MONTH = {July},
ISBN = {1549-9596},
}


Entry last modified by Christine Kiesel, 02/22/2007
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Editor(s)
Andreas Kämper
Created
11/08/2006 01:59:21 PM
Revision
1.
0.


Editor
Christine Kiesel
Andreas Kämper


Edit Date
22.02.2007 15:57:53
11/08/2006 01:59:22 PM