Abstract
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.
In memoriam Antonio Paiva
While we were working on this article, our good friend, colleague, and mentor, Antonio Paiva, died after losing the fight to cancer. We know Antonio as a stimulating force in the GPCR field. He has been one of the founding fathers of the informal GPCR club that met regularly at the EMBL in the early 1990s. The GPCRDB sprouted from these meetings. The thousands of scientists that use the GPCRDB every day owe Antonio thanks. His co-authors will miss him, and send words of condolence to his family. May they find consolation in the fact that the cancer could not stop him from finishing this article. We will miss him.
In memoriam Florence Horn
This paper is a dedication to the memory of Florence Horn who died shortly after we finished this article. Flo did so much to make genomics data come alive in a way that was meaningful to her and to thousands of researchers in bioinformatics, molecular biology, structural biology, and medicinal chemistry. Along with all these researchers, the coauthors of this paper wish to put on record their thanks to Flo and to remember her as a colleague who bestowed her good humor and joie de vivre on all those who worked with her.
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Acknowledgements
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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Paiva†, A.C.M., Oliveira, L., Horn†, F., Bywater, R.P., Vriend, G. (2007). Modeling GPCRs. In: Bourne, H., Horuk, R., Kuhnke, J., Michel, H. (eds) GPCRs: From Deorphanization to Lead Structure Identification. Ernst Schering Foundation Symposium Proceedings, vol 2006/2. Springer, Berlin, Heidelberg. https://doi.org/10.1007/2789_2006_002
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