Theoretical models: Difference between revisions
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Assessment of CASP results is done in a double-blind manner: the predictors do not know the empirical structures, and the assessors do not know the identities of the predictors, which are coded. In CASP8 (<b>2008</b>), there were 13 "template free" targets, that is, sequences for which no significant sequence identity occurred for any empirically solved entry in the [[PDB]]. These are the most difficult to predict, as they must be predicted by ''ab initio'' methods. 102 groups submitted predictions. Assessing the quality of a prediction is not simple, given that even "good" predictions can have high root mean square (RMS) deviations for alpha carbon alignment, e.g. due to a hinge<ref name="casp8" />. Several assessment methods were used, each emphasizing different qualities. A number of groups submitted good predictions for six of the thirteen targets<ref name="casp8">PMID: 19774550</ref>. None of the submitted models was judged to be satisfactory for four of the thirteen templates<ref name="casp8" />. | Assessment of CASP results is done in a double-blind manner: the predictors do not know the empirical structures, and the assessors do not know the identities of the predictors, which are coded. In CASP8 (<b>2008</b>), there were 13 "template free" targets, that is, sequences for which no significant sequence identity occurred for any empirically solved entry in the [[PDB]]. These are the most difficult to predict, as they must be predicted by ''ab initio'' methods. 102 groups submitted predictions. Assessing the quality of a prediction is not simple, given that even "good" predictions can have high root mean square (RMS) deviations for alpha carbon alignment, e.g. due to a hinge<ref name="casp8" />. Several assessment methods were used, each emphasizing different qualities. A number of groups submitted good predictions for six of the thirteen targets<ref name="casp8">PMID: 19774550</ref>. None of the submitted models was judged to be satisfactory for four of the thirteen templates<ref name="casp8" />. | ||
CASP 13 was held in 2018. Excerpts from the conclusions: <ref>Lepore <i>et al.</i>, in press in <i>Proteins: Structure, Function, and Bioinformatics</i>, 2019. DOI: [http://doi.org/10.1002/prot.25805 10.1002/prot.25805]</ref> | CASP 13 was held in 2018. Excerpts from the conclusions: "... the ability of predicting hard protein folds at the tertiary level has increased enormously ..." "On the other hand, important global and local features of prediction models are still seldom as accurate as in the experimental structure. This is the case of enzyme active sites and ligand binding sites, where the predicted arrangement of the amino acids side chains involved in ligand binding and substrate specificity has not achieved the level of accuracy required to confidently infer their function .... Accurate prediction of loops is still a challenging task. As they are often involved in protein interactions, their incorrect prediction can compromise the accuracy of the interacting surface and overall structure of the complex." "... the ability of current methods in modeling the correct quaternary structure of proteins remains rudimentary and shows little progress compared to what observed at the tertiary level."<ref>Lepore <i>et al.</i>, in press in <i>Proteins: Structure, Function, and Bioinformatics</i>, 2019. DOI: [http://doi.org/10.1002/prot.25805 10.1002/prot.25805]</ref> | ||
==See Also== | ==See Also== | ||