title: RaptorX server: a resource for template-based protein structure modeling.
abstract: 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.
authors.affiliation: Toyota Technological Institute, Chicago, IL, USA.
authors.forename: Morten
authors.initials: M
authors.lastname: Källberg
authors.forename: Gohar
authors.initials: G
authors.lastname: Margaryan
authors.forename: Sheng
authors.initials: S
authors.lastname: Wang
authors.forename: Jianzhu
authors.initials: J
authors.lastname: Ma
authors.forename: Jinbo
authors.initials: J
authors.lastname: Xu
mesh_terms: D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D064878:Web Browser
chemical_list: D011506:Proteins