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Sequence searches
The odorant binding proteins listed in this database were identified using the PSI-BLAST approach starting with 10 OBP query sequences from Drosophila melanogaster against all proteins of the three mosquito genomes Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus downloaded from Vectorbase.
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.
Multiple sequence alignments
The multiple sequence alignments provided in this database were constructed using the Clustal X program. The alignments of the proteins were guided by a structural alignment generated using COMPARER with the available structural members in this superfamily. The alignments were truncated based on the structure alignment on the N-terminal end however the C-terminal ends were retained due to the presence of an extended C-terminal in the case of two-domain subfamily members.
Phylogenetic analysis
The phylogenetic trees were inferred using the Neighbor-Joining method in MEGA 4.0. The percentage of replicate trees in which the associated sequences cluster together in the bootstrap test (1000 replicates) are shown next to the branches and 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 was considered as an outgroup. The trees of the different subclasses used for the comparative analysis of the different genomes were analyzed as unrooted trees.
Chromosomal mapping
The figures of the chromosomal mapping were drawn to scale using Adobe illustrator. The genes were mapped to their respective location on the chromosome or supercontigs. The chromosome of Anopheles gambiae is used as reference and are represented as a yellow bar and the contigs of Aedes and Culex are represented in purple and green respectively (supplementary Figures 1a-e). The direct three-way (1:1:1) orthology relationships among the three genomes are represented as green lines. The two-way (1:1) orthology relationships between two species are represented as black lines and the inparalogy relationships are represented as red lines.
Molecular Modelling
The models depicted in this database were derived from rigorous modeling process adapted at various levels by using programs like 3DJURY, Modeller, GROMACS and PROCHECK in template identification, modeling, energy minimization and evaluation respectively.
Molecular docking of Classic OBPs
Docking experiments were carried out on 129 proteins against 125 ligands using AUTODOCK using 48 processors on the cluster facility in the University 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.
The ligand efficience values Ki, LE, FQ and SILE were calculated using the formulae give below
Ki/Inhibition constant
Ligand efficiency
Corrected ligand efficiency
Size independent ligand efficiency
Contact details
Prof Bernard Offmann at University of Nantes
bernard.offmann ‘at’ univ-nantes.fr