Template-based protein structure modeling using the RaptorX web server

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.

Fungal negative-stranded RNA virus that is related to bornaviruses and nyaviruses

“…The protein encoded by ORF I was detected in the protein sample extracted from crude virion preparations (Table S2), and this protein is a possible membrane protein based on analysis with RaptorX web server (23). It is still not clear whether other viral genes code for viral structural proteins due to the extreme fragility of the virions.…”

Novel protein Callipygian defines the back of migrating cells

“…The WDSP WD40-repeat protein structure predictor found a full seven-bladed propeller in the CynA sequence (amino acids 278-616) (31). A seven-bladed propeller structure was also supported by a model of CynA generated by the threading software RaptorX, which found seven adjacent four-strandcontaining β-sheets, although these sheets were separated into two distinct clusters in this model (32). Although CynA lacks sequence homology to proteins in higher eukaryotes, it may have functional homologs because several mammalian proteins share a similar domain composition.…”

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

“…"Constitutive" AS events were detected under different conditions by different techniques and seem unlikely to be random splicing errors. AS events observed in a single condition, on the other hand, potentially include functional, condition-specific (Källberg et al 2012). Five classes of protein sequences were examined: full length annotated proteins, longest proteins predicted from novel TUs, C terminus amino acid sequence starting at the first alteration in AS isoforms and its annotated counterpart, and longest proteins predicted from annotated ncRNA.…”

“…Conservation of novel sequences was assessed by searching for sequence-similar proteins in fission yeasts, fungi, and eukaryotes using BLAST (Gish and States 1993). Secondary and tertiary structures and their properties were predicted by RaptorX (Källberg et al 2012). For 53 novel TUs, we found evidence for homology in other species with less than 100 matching amino acids (Supplemental Fig.…”