Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP

Predicting the three-dimensional structure of a protein from its amino acid sequence is one of the most important current problems of modern biology. The GASP (Critical Assessment of Structure Prediction) blind prediction exp eriments aim to assess the prediction capabilities in the field. A limitati on of GASP is that predictions are prepared and filed by humans using progr ams, and thus, what is being evaluated is the performance of the predicting groups rather than the performance of the programs themselves. To address this limitation the Critical Assessment of Fully Automated Structure Predic tion (CAFASP) experiment was initiated in 1998. In CAFASP, the participants are programs or Internet servers, and what is evaluated are their automati c results without allowing any human intervention. In this paper, we review in brief the current state of protein structure prediction and describe wh at has been learned from the CAFASP1 experiment, the evolution toward CAFAS P2, and how we foresee the future of automated structure prediction. We obs erve that the histories of "in silico" structure prediction experiments and computer chess tournaments show some striking similarities as well as some differences. We question whether the major advances in automated protein s tructure prediction stem from novel insights of the protein folding problem , of protein evolution and function, or merely from the technical advances in the ways the evolutionary information available in the biological databa ses is exploited We conclude with a speculation about the future, where int eresting chess might only be observed in computer games and where the inter pretation of the information encoded in the human genome may be achieved ma inly through in silico biology.