![\"obp_homology_search\"](\"https:\/\/i0.wp.com\/protsci-us2b.univ-nantes.fr\/mobpdb\/wp-content\/uploads\/2012\/04\/obp_homology_search.png?ssl=1\")
<\/a><\/p>\nThe odorant binding proteins listed in this database were identified using the PSI-BLAST<\/a> approach starting with 10 OBP query sequences from Drosophila melanogaster <\/em>against all proteins of the three mosquito genomes Anopheles gambiae,<\/em> Aedes aegypti<\/em> and Culex quinquefasciatus<\/em> downloaded\u00a0from Vectorbase<\/a>.<\/p>\n New hits from any of the three mosquito genomes were re-injected into a psi-blast round. This was re-iterated until no new additional hits were found. \n The multiple sequence alignments provided in this database were constructed using the Clustal X<\/a> program. The alignments of the proteins \u00a0were guided by a structural alignment generated using COMPARER with the available structural members in this superfamily.\u00a0The alignments were truncated based on the structure alignment on the N-terminal end\u00a0however the C-terminal ends were retained due to the presence of an extended C-terminal in the\u00a0case of two-domain <\/em>subfamily members.<\/p>\n \n The phylogenetic trees were inferred using the Neighbor-Joining method<\/a> in MEGA 4.0<\/a>. The percentage of replicate trees in which the associated\u00a0sequences cluster together in the bootstrap test (1000 replicates) are shown next to the branches\u00a0\u00a0and branches with less than 50% bootstrap cutoff were collapsed. The genomic trees were rooted at the branches of a distantly related family of proteins (D7 family of proteins) which\u00a0was considered as an outgroup. The trees of the different subclasses used for the comparative\u00a0analysis of the different genomes were analyzed as unrooted trees.<\/p>\n \n The figures of the chromosomal mapping were drawn to scale using Adobe illustrator. The\u00a0genes were mapped to their respective location on the chromosome or supercontigs. The\u00a0chromosome of Anopheles gambiae <\/em>is used as reference and are represented as a yellow bar and the\u00a0contigs of Aedes <\/em>and Culex <\/em>are represented in purple and green respectively (supplementary Figures\u00a01a-e). The direct three-way (1:1:1) orthology relationships among the three genomes are\u00a0represented as green<\/strong><\/span> lines. The two-way (1:1) orthology relationships between two species are\u00a0represented as black<\/strong> lines and the inparalogy relationships are represented as red<\/strong> <\/span>lines.<\/p>\n \n The models depicted in this database were derived from rigorous modeling process adapted at various levels by using programs like 3DJURY<\/a>, Modeller<\/a>, GROMACS<\/a> and PROCHECK <\/a>in template identification, modeling, energy minimization and evaluation respectively.<\/p>\n \n Docking experiments were carried out on 129 proteins against 125 ligands using AUTODOCK<\/a> using 48 processors on the cluster facility in the\u00a0University of de La Reunion. The ligand binding profiles and cluster based plots were generated using the R program. The graphical representation of the interacting residues were built using LIGPLOT<\/a>.<\/p>\n The ligand efficience values Ki, LE, FQ and SILE were calculated using the formulae give below<\/p>\n Ki\/Inhibition constant<\/strong><\/p>\n Ligand efficiency<\/strong><\/p>\n Corrected ligand efficiency<\/strong><\/p>\n
\n<\/a><\/p>\nMultiple sequence alignments<\/strong><\/h3>\n
<\/a><\/p>\nPhylogenetic analysis<\/strong><\/h3>\n
Chromosomal mapping<\/strong><\/h3>\n
Molecular Modelling<\/strong><\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nMolecular docking \u00a0of Classic <\/em>OBPs<\/strong><\/h3>\n
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