OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

Yinghao Wu, Athanasios D. Dousis, Mingzhi Chen, Jialin Li, Jianpeng Ma

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.

Original languageEnglish (US)
Pages (from-to)1314-1329
Number of pages16
JournalJournal of Molecular Biology
Issue number4
StatePublished - Jan 30 2009
Externally publishedYes


  • chain skeleton
  • domain boundary
  • protein folding
  • statistical scores
  • structure prediction

ASJC Scopus subject areas

  • Molecular Biology
  • Biophysics
  • Structural Biology


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