期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 385, 期 4, 页码 1314-1329出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2008.10.093
关键词
protein folding; structure prediction; chain skeleton; statistical scores; domain boundary
资金
- National Institutes of Health [R01-GM067801]
- National Science Foundation [MCB-0818353]
- Welch Foundation [Q-1512]
- Doer Foundation
- Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia
- Keck Center through the National Library of Medicine Computational Biology and Medicine Training Program (NLM) [5T15LM07093]
- NSF [EIA-0216467]
- Intel
- HP
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0818353] Funding Source: National Science Foundation
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. (C) 2008 Elsevier Ltd. All rights reserved.
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