OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries |
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Authors: | Yinghao Wu Athanasios D Dousis Mingzhi Chen Jialin Li |
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Institution: | 1 Department of Bioengineering, Rice University, Houston, TX 77005, USA 2 Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA 3 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA |
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Abstract: | 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. |
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Keywords: | SSE secondary-structure element SSSM super secondary structure motif MC Monte Carlo DLI domain linker index REI residue entropy index GHL George and Heringa linker index KDH Kyte and Doolittle hydropathy index ARM DLI+REI consensus domain predictor Armadillo GM Galzitskaya and Melnik SCOP Structural Classification of Proteins DBPL domain boundary profile library |
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