期刊
NATURE PROTOCOLS
卷 7, 期 8, 页码 1511-1522出版社
NATURE PORTFOLIO
DOI: 10.1038/nprot.2012.085
关键词
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资金
- US National Institutes of Health [R01GM0897532]
- US National Science Foundation [DBI-0960390]
- Microsoft
- FMC
- Toyota Technical Institute at Chicago
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0960390] Funding Source: National Science Foundation
A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX similar to 35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed similar to 6,000 sequences submitted by similar to 1,600 users from around the world.
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