Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 58, Issue 2, Pages 321-328Publisher
WILEY
DOI: 10.1002/prot.20308
Keywords
fold recognition; protein threading; protein structure prediction; sequence profile
Categories
Funding
- NIGMS NIH HHS [R01 GM 966049, R01 GM066049, R01 GM 068530, R01 GM068530] Funding Source: Medline
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Recognizing structural similarity without significant sequence identity has proved to be a challenging task. Sequence-based and structure-based methods as well as their combinations have been developed. Here, we propose a fold-recognition method that incorporates structural information without the need of sequence-to-structure threading. This is accomplished by generating sequence profiles from protein structural fragments. The structure-derived sequence profiles allow a simple integration with evolution-derived sequence profiles and secondary-structural information for an optimized alignment by efficient dynamic programming. The resulting method (called SP3) is found to make a statistically significant improvement in both sensitivity of fold recognition and accuracy of alignment over the method based on evolution-derived sequence profiles alone (SP) and the method based on evolution-derived sequence profile and secondary structure profile (SP2). SP3 was tested in SALIGN benchmark for alignment accuracy and Lindahl, PROSPECTOR 3.0, and LiveBench 8.0 benchmarks for remote-homology detection and model accuracy. Sp(3) is found to be the most sensitive and accurate single-method server in all benchmarks tested where other methods are available for comparison (although its results are statistically indistinguishable from the next best in some cases and the comparison is subjected to the limitation of time-dependent sequence and/or structural library used by different methods.). In LiveBench 8.0, its accuracy rivals some of the consensus methods such as ShotGunINBGU, Pmodeller3, Pcons4, and ROBETTA. (C) 2004 Wiley-Liss, Inc.
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