Computational protocol: Computational reverse chemical ecology: Virtual screening and predicting behaviorally active semiochemicals for Bactrocera dorsalis

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Protocol publication

[…] During our homology search an antenna OBP of Bactrocera dorsalis with homology to our isolated protein existed in the protein sequence database (GenBank ID: ACB56577.1) of the National Centre for Biotechnology Information. A thorough search for the three dimensional structure of the OBP in PDB (Protein Database: http://www.rcsb.org/pdb) ascertained the non-existence of 3D structure of this protein. Therefore, the complete OBP submitted in GenBank was used for construction of a 3D model for our in-silico docking studies. Three-dimensional modelling of the antennal OBP of B. dorsalis was developed using an online protein threading (PHYRE 2) and homology modelling (SWISS-MODEL) online programs. AgamOBP1, a female odorant binding protein from Anopheles gambiae (PDB code: 2ERB) [], CquiOBP1, a female-dominant odorant binding protein from Culex quinquefasciatus (PDB code: 3OGN) [,] and AaegOBP1, a major female- enriched odorant-binding protein from Aedes aegypti (PDB code: 3K1E) [] were suggested as templates by the program. Multiple sequence alignment of the OBPs was carried out using Clustal O (see Additional file ). It was found that the proteins had a identity of 48.993%. Identical and similar positions were 73 and 36 respectively. Based on the identified structural templates and the corresponding sequences, several 3D models were constructed using Modeler module in Discovery Studio 2.0 (Accelrys Software Inc., USA). The unaligned residues were deleted and the proteins were refined. The profiles-3D method was used as a standard in evaluating the fitness between the sequences and the 3D models. The model with the highest score of profile-3D was optimized and considered for further processing. Multiple sequence alignment (MSA) of the protein sequence used in the study is provided (see Additional file ). […]

Pipeline specifications

Software tools Phyre, SWISS-MODEL
Application Protein structure analysis
Organisms Bactrocera dorsalis, Ilex paraguariensis
Chemicals Pheromones