Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server (http://raptorx.uchicago.edu), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling. Given a target sequence, RaptorX server is able to detect even remotely related template sequences by means of a novel nonlinear context-specifi c alignment potential and probabilistic consistency algorithm. Using the protocol presented here it is thus possible to obtain high-quality structural models for many target protein sequences when only distantly related protein domains have experimentally solved structures. At present, RaptorX server can perform secondary and tertiary structure prediction of a 200 amino acid target sequence in approximately 30 min.
CITATION STYLE
Källberg, M., Margaryan, G., Wang, S., Ma, J., & Xu, J. (2014). Raptorx server: A resource for template-based protein structure modeling. Methods in Molecular Biology, 1137, 17–27. https://doi.org/10.1007/978-1-4939-0366-5_2
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