publication . Article . Other literature type . 2012

Template-based protein structure modeling using the RaptorX web server

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo;
Open Access
  • Published: 19 Jul 2012 Journal: Nature Protocols, volume 7, pages 1,511-1,522 (issn: 1754-2189, eissn: 1750-2799, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
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 (espec...
Subjects
free text keywords: Bioinformatics, Cell biology, Biology, Protein tertiary structure, Structural alignment, Protein function prediction, Data mining, computer.software_genre, computer, Server, Protein structure prediction, Protein structure database, Structural genomics, Web server, Article
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