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Author, Editor(s)

Author(s):

Hartmann, Christoph
Antes, Iris
Lengauer, Thomas

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BibTeX cite key*:

Hartmann2007

Title

Title*:

IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.

Journal

Journal Title*:

Protein Science

Journal's URL:

http://www.proteinscience.org/

Download URL
for the article:

http://www.proteinscience.org/cgi/reprint/16/7/1294

Language:

English

Publisher

Publisher's
Name:

Protein Society

Publisher's URL:

http://www.proteinsociety.org/

Publisher's
Address:


ISSN:


Vol, No, pp, Date

Volume*:

16

Number:


Publishing Date:

2007

Pages*:

1294-1307

Number of
VG Pages:


Page Start:


Page End:


Sequence Number:


DOI:

10.1110/ps.062658307

Note, Abstract, ©

Note:


(LaTeX) Abstract:

We introduce a new algorithm, IRECS (Iterative REduction of Conformational Space), for identifying ensembles of most probable side-chain conformations for homology modeling. On the basis of a given rotamer library, IRECS ranks all side-chain rotamers of a protein according to the probability with which each side chain adopts the respective rotamer conformation. This ranking enables the user to select small rotamer sets that are most likely to contain a near-native rotamer for each side chain. IRECS can therefore act as a fast heuristic alternative to the Dead-End-Elimination algorithm (DEE). In contrast to DEE, IRECS allows for the selection of rotamer subsets of arbitrary size, thus being able to define structure ensembles for a protein. We show that the selection of more than one rotamer per side chain is generally meaningful, since the selected rotamers represent the conformational space of flexible side chains. A knowledge-based statistical potential ROTA was constructed for the IRECS algorithm. The potential was optimized to discriminate between side-chain conformations of native and rotameric decoys of protein structures. By restricting the number of rotamers per side chain to one, IRECS can optimize side chains for a single conformation model. The average accuracy of IRECS for the $\chi_1$ and $\chi_{1+2}$ dihedral angles amounts to 84.7\% and 71.6\%, respectively, using a 40 degrees cutoff. When we compared IRECS with SCWRL and SCAP, the performance of IRECS was comparable to that of both methods. IRECS and the ROTA potential are available for download from the URL http://irecs.bioinf.mpi-inf.mpg.de.

URL for the Abstract:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&uid=17567749&cmd=showdetailview&indexed=google

Categories,
Keywords:


HyperLinks / References / URLs:


Copyright Message:


Personal Comments:


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Access Level:

Internal

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Appearance:

MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort


BibTeX Entry:

@ARTICLE{Hartmann2007,
AUTHOR = {Hartmann, Christoph and Antes, Iris and Lengauer, Thomas},
TITLE = {{IRECS}: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.},
JOURNAL = {Protein Science},
PUBLISHER = {Protein Society},
YEAR = {2007},
VOLUME = {16},
PAGES = {1294--1307},
DOI = {10.1110/ps.062658307},
}


Entry last modified by Joachim Büch, 02/28/2008
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Editor(s)
Christoph Hartmann
Created
12/11/2007 04:38:50 PM
Revision
1.
0.


Editor
Joachim Büch
Christoph Hartmann


Edit Date
02.01.2008 18:53:40
12/11/2007 04:38:50 PM