HHalign-Kbest

HHalign-Kbest is a tool that implements a novel algorithm for generating k-best suboptimal hidden Markov model (HMM)-HMM alignments, rather than only the optimal one, and evaluating the corresponding structural models to improve alignment accuracy. The method was benchmarked over 420 targets from the SCOP30 database, and it was found that the quality of the models (TM-score) raised by 4.1-16.3% and 8.0-21.0% considering the top 1 and top 10 best models, respectively, in the range of HHsearch probability of 20-99%.

Topic

Structure analysis;Protein structure analysis;Protein folds and structural domains

Detail

  • Operation: Protein modelling;Optimisation and refinement;Structure alignment

  • Software interface: Command-line user interface;Web user interface

  • Language: Perl

  • License: Web application

  • Cost: Free

  • Version name: -

  • Credit: ANR-IAB-2011 ‘BIP-BIP’ and IDEX Paris Saclay—IDI 2013

  • Input: -

  • Output: -

  • Contact: Raphael Guerois guerois@cea.fr

  • Collection: -

  • Maturity: -

Publications

  • HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling.
  • Yu J, et al. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. 2015; 31:3850-2. doi: 10.1093/bioinformatics/btv441
  • https://doi.org/10.1093/bioinformatics/btv441
  • PMID: 26231431
  • PMC: -

Download and documentation

< Back to DB search