Introduction

SUMMARY: Recently, several new contact prediction methods have been published. They use (i) large sets of multiple aligned sequences and (ii) assume that correlations between columns in these alignments can be the results of indirect interaction. These methods are clearly superior to earlier methods when it comes to predicting contacts in proteins. Here, we demonstrate that combining predictions from two prediction methods, PSICOV and plmDCA, and two alignment methods, HHblits and jackhmmer at four different e-value cut-offs, provides a relative improvement of 20% in comparison with the best single method, exceeding 70% correct predictions for one contact prediction per residue. AVAILABILITY: The source code for PconsC along with supplementary data is freely available at http://c.pcons.net/ CONTACT: arne@bioinfo.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. PconsC: combination of direct information methods and alignments improves contact prediction.
    Cite this
    Skwark MJ, Abdel-Rehim A, Elofsson A, 2013-07-01 - Bioinformatics (Oxford, England)
  2. Improved contact predictions using the recognition of protein like contact patterns.
    Cite this
    Skwark MJ, Raimondi D, Michel M, Elofsson A, 2014-11-01 - PLoS computational biology

Credits

  1. Marcin J Skwark
    Developer

    Department of Biochemistry and Biophysics, Stockholm University, Sweden

  2. Abbi Abdel-Rehim
    Developer

  3. Arne Elofsson
    Investigator

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Summary
AccessionBT000289
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByArne Elofsson