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Abstract
Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.
Highlights
Transitivity of sequence homology by using profiles for both target and template and, become more sensitive than profile-to-sequence alignments[13,14,15]
These improvements increase the true positive rate (TPR) of template detection by 5% compared to the initial version of ORION for 10% of false positive rate (FPR)
A collection of ORION templates profiles based on the protein data bank (PDB), which contains all available 3D structures of proteins, filtered with a maximum sequence identity of 95% or 70%
Summary
Transitivity of sequence homology by using profiles for both target and template and, become more sensitive than profile-to-sequence alignments[13,14,15]. Combining sequence and structure information into a hybrid profile is a better approach for the detection of distant homology relationships[22]. ORION is a fold recognition method based on the pairwise comparison of profiles combining sequence and structural information recently developed in our group[22]. It relies on a better description of the local protein structure to boost distantly protein detection. Thanks to PB structural descriptor and hybrid profile-profile comparisons, ORION outperforms, in terms of template detection sensitivity at fold level, profile-sequence methods like PSI-BLAST by 16% more and profile-profile methods like HHsearch by 5% more[22]. We present here the ORION web server, freely usable for scientific and academic community, along with our new and improved approach
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