Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation

Chun Fang*, Tamotsu Noguchi, Hayato Yamana

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


Background: Identifying ligand-binding sites is a key step to annotate the protein functions and to find applications in drug design. Now, many sequence-based methods adopted various predicted results from other classifiers, such as predicted secondary structure, predicted solvent accessibility and predicted disorder probabilities, to combine with position-specific scoring matrix (PSSM) as input for binding sites prediction. These predicted features not only easily result in high-dimensional feature space, but also greatly increased the complexity of algorithms. Moreover, the performances of these predictors are also largely influenced by the other classifiers.Results: In order to verify that conservation is the most powerful attribute in identifying ligand-binding sites, and to show the importance of revising PSSM to match the detailed conservation pattern of functional site in prediction, we have analyzed the Adenosine-5'-triphosphate (ATP) ligand as an example, and proposed a simple method for ATP-binding sites prediction, named as CLCLpred (Contextual Local evolutionary Conservation-based method for Ligand-binding prediction). Our method employed no predicted results from other classifiers as input; all used features were extracted from PSSM only. We tested our method on 2 separate data sets. Experimental results showed that, comparing with other 9 existing methods on the same data sets, our method achieved the best performance.Conclusions: This study demonstrates that: 1) exploiting the signal from the detailed conservation pattern of residues will largely facilitate the prediction of protein functional sites; and 2) the local evolutionary conservation enables accurate prediction of ATP-binding sites directly from protein sequence.

Original languageEnglish
Article number7
JournalAlgorithms for Molecular Biology
Issue number1
Publication statusPublished - 2014 Mar 11


  • ATP-binding site
  • Local evolutionary conservation
  • Sequence-based

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics


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