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Proceedings Article, Paper
@InProceedings
Beitrag in Tagungsband, Workshop

Author, Editor
Author(s):
Althaus, Ernst
Kohlbacher, Oliver
Lenhof, Hans-Peter
Müller, Peter
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Editor(s):
Shamir, Ron
Miyano, Satoru
Istrail, Sorin
Pevzner, Pavel
Waterman, Michael
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BibTeX cite key*:
AKL+2000
Title, Booktitle
Title*:
A Combinatorial Approach to Protein Docking with Flexible Side-Chains
Booktitle*:
Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00)
Event, URLs
Conference URL::
http://recomb2000.ims.u-tokyo.ac.jp/
Downloading URL:
Event Address*:
Tokyo, Japan
Language:
English
Event Date*
(no longer used):
April 8-11, 2000
Organization:
Association for Computing Machinery (ACM SIGACT)
Event Start Date:
Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected
Event End Date:
Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected Incorrect data type for operator or @Function: Time/Date expected
Publisher
Name*:
ACM Press
URL:
http://www.acm.org/
Address*:
New York, USA
Type:
Vol, No, Year, pp.
Series:
Volume:
Number:
Month:
April
Pages:
15-24
Year*:
2000
VG Wort Pages:
ISBN/ISSN:
1-58113-186-0
Sequence Number:
DOI:
Note, Abstract, ©
(LaTeX) Abstract:
\begin{abstract}
Rigid body docking approaches are not sufficient to predict the structure of a
protein complex from the unbound (native) structures of the two proteins.
Accounting for side--chain flexibility is an important step towards fully
flexible protein docking. This work describes an approach that allows
conformational flexibility for the side--chains while keeping the protein
backbone rigid. Starting from candidates created by a rigid docking
algorithm, we demangle the side--chains of the docking site, thus creating
reasonable approximations of the true complex structure. These structures are
ranked with respect to the binding free energy. We present two new techniques
for side--chain demangling. Both approaches are based on a discrete
representation of the side--chain conformational space by the use of a rotamer
library. This leads to a combinatorial optimization problem. For the solution
of this problem we propose a fast heuristic approach and an exact, albeit
slower method using branch--\&--cut techniques. As a test set we use the
unbound structures of three proteases and the corresponding protein
inhibitors. For each of the examples the highest--ranking conformation
produced was a good approximation of the true complex structure.
\end{abstract}
Keywords:
Computational Molecular Biology, Docking, Combinatorial Optimization
Download
Access Level:
Public

Correlation
MPG Unit:
Max-Planck-Institut für Informatik
MPG Subunit:
Algorithms and Complexity Group
Audience:
Expert
Appearance:
MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat



BibTeX Entry:

@INPROCEEDINGS{AKL+2000,
AUTHOR = {Althaus, Ernst and Kohlbacher, Oliver and Lenhof, Hans-Peter and M{\"u}ller, Peter},
EDITOR = {Shamir, Ron and Miyano, Satoru and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
TITLE = {A Combinatorial Approach to Protein Docking with Flexible Side-Chains},
BOOKTITLE = {Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00)},
PUBLISHER = {ACM Press},
YEAR = {2000},
ORGANIZATION = {Association for Computing Machinery (ACM SIGACT)},
PAGES = {15--24},
ADDRESS = {Tokyo, Japan},
MONTH = {April},
ISBN = {1-58113-186-0},
}


Entry last modified by Christine Kiesel, 03/02/2010
Hide details for Edit History (please click the blue arrow to see the details)Edit History (please click the blue arrow to see the details)

Editor(s)
Oliver Kohlbacher
Created
04/17/2000 11:58:55 AM
Revisions
4.
3.
2.
1.
0.
Editor(s)
Christine Kiesel
Uwe Brahm
Anja Becker
Anja Becker
Anja Becker
Edit Dates
02.05.2007 17:59:16
05/02/2001 12:06:41 PM
23.03.2001 13:17:39
20.03.2001 17:04:13
17/04/2000 11:58:55