Journal Article
@Article
Artikel in Fachzeitschrift


Show entries of:

this year (2019) | last year (2018) | two years ago (2017) | Notes URL

Action:

login to update

Options:




Library Locked Library locked




Author, Editor(s)

Author(s):

Wohlers, Inken
Domingues, Francisco S.
Klau, Gunnar W.

dblp
dblp
dblp

Not MPG Author(s):

Wohlers, Inken
Klau, Gunnar W.

BibTeX cite key*:

Wohlers2010

Title

Title*:

Towards optimal alignment of protein structure distance matrices

Journal

Journal Title*:

Bioinformatics

Journal's URL:

http://bioinformatics.oxfordjournals.org/

Download URL
for the article:

http://dx.doi.org/10.1093/bioinformatics/btq420

Language:

English

Publisher

Publisher's
Name:

Oxford University Press

Publisher's URL:

http://www.oup.com/

Publisher's
Address:

Oxford, UK

ISSN:

1367-4803

Vol, No, pp, Date

Volume*:

26

Number:

18

Publishing Date:

September 2010

Pages*:

2273-2280

Number of
VG Pages:


Page Start:

2273

Page End:

2280

Sequence Number:


DOI:

10.1093/bioinformatics/btq420

Note, Abstract, ©

Note:


(LaTeX) Abstract:

MOTIVATION: Structural alignments of proteins are important for identification of structural similarities, homology detection and functional annotation. The structural alignment problem is well studied and computationally difficult. Many different scoring schemes for structural similarity as well as many algorithms for finding high-scoring alignments have been proposed. Algorithms using contact map overlap (CMO) as scoring function are currently the only practical algorithms able to compute provably optimal alignments. RESULTS: We propose a new mathematical model for the alignment of inter-residue distance matrices, building upon previous work on maximum CMO. Our model includes all elements needed to emulate various scoring schemes for the alignment of protein distance matrices. The algorithm that we use to compute alignments is practical only for sparse distance matrices. Therefore, we propose a more effective scoring function, which uses a distance threshold and only positive structural scores. We show that even under these restrictions our approach is in terms of alignment accuracy competitive with state-of-the-art structural alignment algorithms, whereas it additionally either proves the optimality of an alignment or returns bounds on the optimal score. Our novel method is freely available and constitutes an important promising step towards truly provably optimal structural alignments of proteins. AVAILABILITY: An executable of our program PAUL is available at http://planet-lisa.net/.

URL for the Abstract:

http://bioinformatics.oxfordjournals.org/content/26/18/2273.abstract

Categories,
Keywords:


HyperLinks / References / URLs:


Copyright Message:


Personal Comments:


Download
Access Level:

Internal

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{Wohlers2010,
AUTHOR = {Wohlers, Inken and Domingues, Francisco S. and Klau, Gunnar W.},
TITLE = {Towards optimal alignment of protein structure distance matrices},
JOURNAL = {Bioinformatics},
PUBLISHER = {Oxford University Press},
YEAR = {2010},
NUMBER = {18},
VOLUME = {26},
PAGES = {2273--2280},
ADDRESS = {Oxford, UK},
MONTH = {September},
ISBN = {1367-4803},
DOI = {10.1093/bioinformatics/btq420},
}


Entry last modified by Anja Becker, 01/18/2011
Show details for Edit History (please click the blue arrow to see the details)Edit History (please click the blue arrow to see the details)
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)
[Library]
Created
11/26/2010 12:32:29 PM
Revisions
2.
1.
0.

Editor(s)
Anja Becker
Anja Becker
Francisco S. Domingues

Edit Dates
18.01.2011 09:37:58
14.01.2011 15:29:37
11/26/2010 12:32:29 PM