Many GPCR models have been built over the years for many different purposes, of which drug-design undoubtedly has been the most frequent one. The release of the structure of bovine rhodopsin in August 2000 enabled us to analyze models built before that period to learn things for the models we build today. We conclude that the GPCR modeling field is riddled with “common knowledge”. Several characteristics of the bovine rhodopsin structure came as a big surprise, and had obviously not been predicted, which led to large errors in the models. Some of these surprises, however, could have been predicted if the modelers had more rigidly stuck to the rule that holds for all models, namely that a model should explain all experimental facts, and not just those facts that agree with the modeler's preconceptions.
KeywordsTransmembrane Helix Residue Numbering System Bovine Rhodopsin Structure Superposition Ocular Albinism
The GPCRDB was initiated as an EC sponsored project (PL 950224). GV acknowledges financial support from BioRange and BioSapiens. The BioSapiens project is funded by the European Commission within its FP6 Programme, under the thematic area “Life sciences, genomics and biotechnology for health,” contract number LSHG-CT-2003–503265. BioRange is a programme of the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI).
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