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Template-based protein structure modeling using the RaptorX web server
Open accessAbstract
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 ∼35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ∼6,000 sequences submitted by ∼1,600 users from around the world.
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Metadata
- Authors
- Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., & Xu, J.
- Venue
- Nature Protocols
- Published
- 2012-07-19
- Volume
- 7
- Issue
- 8
- Pages
- 1511-1522
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W1981264193
- Cited by
- 1,597
- References
- 4
- FWCI
- 20.45
- Type
- journal article
- Language
- en
- Open access
- green
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