Template-based protein structure modeling using the RaptorX web server

Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu, Jinbo Xu

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1511-1522
Number of pages12
JournalNature Protocols
Issue number8
StatePublished - Aug 2012
Externally publishedYes

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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