Theoretical models: Difference between revisions

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The success of fold prediction methods is assessed biannually in the ''Critical Assessment of Techniques for Protein Structure Prediction'' (CASP) competitions<ref>[http://predictioncenter.gc.ucdavis.edu/ Critical Assessment of Techniques for Protein Structure Prediction (CASP)].</ref>. Crystallographers submit sequences which they have solved, but for which the structures have not yet been published. Modelers predict the folds which are then compared with subsequently published structures. Beginning in CASP5 (2002), the ability to predict [[Intrinsically Disordered Protein|intrinsic disorder]] was included<ref>PMID: 19774619</ref>. There are also competitions to predict protein-protein docking interactions<ref>[http://www.ebi.ac.uk/msd-srv/capri/ CAPRI: Critical Assessment of PRediction of Interactions].</ref>

In 2005, for about one out of four cases of small domains of less than 85 amino acids, the best predictions were within about 1.5 Å (RMS for carbon alphas) of the true structure<ref>PMID: 16166519</ref>. (Independent determinations of the same protein by empirical methods generally agree within about 0.5 Å RMS for carbon alphas.)

In 2005, for about one out of four cases of small domains of less than 85 amino acids, the best predictions were within about 1.5 Å (RMS for carbon alphas) of the true structure<ref>PMID: 16166519</ref>. (Independent determinations of the same protein by empirical methods generally agree within about 0.5 Å RMS for carbon alphas.)

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 (2008), 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 (2008), 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 et al., in press in Proteins: Structure, Function, and Bioinformatics, 2019. DOI: [http://doi.org/10.1002/prot.25805 10.1002/prot.25805]</ref>

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Theoretical models: Difference between revisions

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 The success of fold prediction methods is assessed biannually in the ''Critical Assessment of Techniques for Protein Structure Prediction'' (CASP) competitions<ref>[http://predictioncenter.gc.ucdavis.edu/ Critical Assessment of Techniques for Protein Structure Prediction (CASP)].</ref>. Crystallographers submit sequences which they have solved, but for which the structures have not yet been published. Modelers predict the folds which are then compared with subsequently published structures. Beginning in CASP5 (2002), the ability to predict [[Intrinsically Disordered Protein|intrinsic disorder]] was included<ref>PMID: 19774619</ref>. There are also competitions to predict protein-protein docking interactions<ref>[http://www.ebi.ac.uk/msd-srv/capri/ CAPRI: Critical Assessment of PRediction of Interactions].</ref>
-In 2005, for about one out of four cases of small domains of less than 85 amino acids, the best predictions were within about 1.5 &Aring; (RMS for carbon alphas) of the true structure<ref>PMID: 16166519</ref>. (Independent determinations of the same protein by empirical methods generally agree within about 0.5 &Aring; RMS for carbon alphas.)
+In <b>2005</b>, for about one out of four cases of small domains of less than 85 amino acids, the best predictions were within about 1.5 &Aring; (RMS for carbon alphas) of the true structure<ref>PMID: 16166519</ref>. (Independent determinations of the same protein by empirical methods generally agree within about 0.5 &Aring; RMS for carbon alphas.)
-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 (2008), 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>
 ==See Also==