Template-based protein structure modeling using the RaptorX web server

• Published in: Nature protocols Vol. 7; no. 8; pp. 1511 - 1522
• Main Authors: Källberg, Morten, Wang, Haipeng, Wang, Sheng, Peng, Jian, Wang, Zhiyong, Lu, Hui, Xu, Jinbo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.08.2012; Nature Publishing Group
• Subjects: 631/114/2411; 631/1647/48; 82/81; Algorithms; Alignment; Amino acids; Analytical Chemistry; Biological Techniques; Computational Biology - methods; Computational Biology/Bioinformatics; Internet server software; Life Sciences; Microarrays; Modelling; Models, Molecular; Organic Chemistry; Probability theory; Protein Conformation; Protein structure; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Proteins - chemistry; Proteomes; Protocol; Quality assessment; Quality control; Secondary structure; Software; Structural models; Structure; Tertiary structure; Three dimensional models; United States; United States > US; Illinois; Chicago Illinois
• ISSN: 1754-2189; 1750-2799; 1750-2799
• DOI: 10.1038/nprot.2012.085

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.