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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

URL of the conference:

http://recomb2000.ims.u-tokyo.ac.jp/

URL for downloading the paper:


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:

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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
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Editor(s)
Oliver Kohlbacher
Created
04/17/2000 11:58:55 AM
Revisions
4.
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1.
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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
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