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RaptorX server: A Resource for Template-Based Protein Structure Modeling

2014; Springer Science+Business Media; Linguagem: Inglês

10.1007/978-1-4939-0366-5_2

1940-6029

Morten Källberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma, Jinbo Xu,

RNA and protein synthesis mechanisms

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-specific 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.