ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

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/.

Peptides Based Vaccine Against SARS-nCoV-2 Antigenic Fragmented Synthetic Epitopes Recognized by T-Cell and β-Cell initiate Specific Antibody to Fight the Infection

“…Synthetic peptide vaccines candidate of antigenic epitope fragments peptides sequence were to alignment accuracy, fold recognition and structure prediction by using several benchmarks that were determined by SPARKS-X (Yuedong et al, 2011): Protein fold recognition and ORION: Optimized protein fold Recognition (Ghouzam et al, 2015;Ghouzam et al, 2016). In addition, PAComplex server to predict a peptide antigens and search the template-based homologous speci c peptide antigens of our query short vaccine candidate peptide amino acid sequence by the following methods (Liu et al, 2011).…”

Peer Review #1 of "PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks (v0.1)"

“…PBs are also useful to compare and superimpose protein structures with pairwise and multiple approaches (Joseph et al, 2011(Joseph et al, , 2012, namely iPBA (Gelly et al, 2011) and mulPBA (Léonard et al, 2014), both currently showing best results compared to other superimposition methods. Eventually, PBs lead to interesting results at predicting protein structures from their sequences (Ghouzam et al, 2015(Ghouzam et al, , 2016) and at predicting protein flexibility (Bornot et al, 2011;de Brevern et al, 2012).…”

ANNAVP, using neural networks to predict neutralization efficiency of antibodies against viral strains and to cluster strains by protein sequence

“…The binding affinity between two proteins cannot be directly deduced from their amino acid sequences, due to their secondary and tertiary structures also contributing to said affinity. Difficulties are especially brought by the tertiary structure, whose deduction from the amino acid sequence is an on-going problem in bioinformatics (Ghouzam et al, 2016;Qian & Sejnowski, 1988;Rost & Sander, 1993).…”