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.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Källberg M,Wang H,Wang S,Peng J,Wang Z,Lu H,Xu Jdoi
10.1038/nprot.2012.085subject
Has Abstractpub_date
2012-07-19 00:00:00pages
1511-22issue
8eissn
1754-2189issn
1750-2799pii
nprot.2012.085journal_volume
7pub_type
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