Using the aligned structures a 3D-model of the ligand binding site of the σ1 receptor was obtained, whose general features are in good agreement with previous assumptions on the receptor structure, but revealed some novel insights since it represents the receptor surface in more detail.
DAMSUP was used to align all models with the most probable one, and all of the aligned models were averaged in DAMAVER to compute a probability map.
Using the aligned sequences and the best-fit models of nucleotide substitution, we estimated a maximum likelihood phylogeny using the PHYML algorithm with a BIONJ starting tree [43], [44].
In practice, the focus of many users of 3D models is not just on retrieval performance, but the use of aligned models for different purposes.
Sequences were aligned using the codon model in the PRANK Probabilistic Alignment Kit [ 59].
The cDNA sequences were aligned using the codon model of program PRANK (100701 version) using the default options [ 52], and were then translated into amino acid sequences.
The coding sequences were aligned using the codon model of PRANK software (100701 version) using the default options [ 52], and alignment gaps were deleted manually.
brevicollis, O. carmela, C. nucula, E. muelleri, Suberites domuncula, A. queenslandica, T. adhaerens, Hydra magnapapillata, Anopheles gambiae, Caenorhabditis elegans, Strongylocentrotus purpuratus, and H. sapiens were aligned using the TRNA2 model in the COVE package (Eddy and Durbin 1994).
Alignments for the model, generated using the Modeller align function, were altered manually to provide the best representative alignment.
Alignments for the model were generated using the Modeler align function.
