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Template-based protein structure modeling using the RaptorX web server

Nature Protocols volume 7, pages 1511–1522 (2012)Cite this article

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Abstract

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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Figure 1: Performance assessment of core prediction modules in the RaptorX server.
Figure 2: Workflow used by the RaptorX server.
Figure 3: Job-listing interface.
Figure 4: Secondary structure result interface.
Figure 5: Tertiary structure result interface.
Figure 6: Disorder prediction result display.
Figure 7: Custom alignment result interface.
Figure 8: Domain parsing result display.

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Acknowledgements

This work is supported by the US National Institutes of Health grants R01GM0897532, a US National Science Foundation grant DBI-0960390, a Microsoft PhD Research Fellowship, an FMC Educational Fund Fellowship and the Toyota Technical Institute at Chicago summer intern program. We are grateful to the University of Chicago Beagle team, TeraGrid and Canada's Shared Hierarchical Academic Research Computing Network (SHARCNet) for their support of computational resources.

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Author notes

  1. Morten Källberg and Haipeng Wang: These authors contributed equally to this work.

Authors and Affiliations

  1. Toyota Technological Institute at Chicago, Chicago, Illinois, USA

    Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang & Jinbo Xu

  2. Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA

    Morten Källberg & Hui Lu

Authors
  1. Morten Källberg
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Contributions

J.X. conceived and supervised the project. M.K. and H.W. designed and developed the web server. H.L. oversaw server development. J.P. developed the threading algorithm. S.W. designed the template database. Z.W. developed the protein secondary structure prediction algorithm. M.K. and J.X. wrote the paper.

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Correspondence to Jinbo Xu.

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Källberg, M., Wang, H., Wang, S. et al. Template-based protein structure modeling using the RaptorX web server. Nat Protoc 7, 1511–1522 (2012). https://doi.org/10.1038/nprot.2012.085

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