English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  bbcontacts: Prediction of β-strand pairing from direct coupling patterns.

Andreani, J., & Söding, J. (2015). bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics, 31(11), 1729-1737. doi:10.1093/bioinformatics/btv041.

Item is

Files

show Files
hide Files
:
2086522.pdf (Publisher version), 706KB
Name:
2086522.pdf
Description:
-
OA-Status:
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-
:
2086522_Suppl.pdf (Supplementary material), 14MB
Name:
2086522_Suppl.pdf
Description:
-
OA-Status:
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Creators

show
hide
 Creators:
Andreani, J.1, Author           
Söding, J.1, Author           
Affiliations:
1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              

Content

show
hide
Free keywords: -
 Abstract: Motivation: It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β-β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs. Results: bbcontacts predicts β-β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modeled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with <1000 sequences, bbcontacts achieves 50% precision for contacting β-β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure. Availability: bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts

Details

show
hide
Language(s): eng - English
 Dates: 2015-01-23
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/bioinformatics/btv041
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 31 (11) Sequence Number: - Start / End Page: 1729 - 1737 Identifier: -