Theoretical models: Difference between revisions

Line 32:

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>

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~~. A number of groups submitted good predictions for six of the thirteen targets. None of the submitted models was judged to be satisfactory for four of the thirteen templates~~. 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.

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" />. 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" />.

==See Also==

Theoretical models: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 32: / Line 32: @@
 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>
-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. A number of groups submitted good predictions for six of the thirteen targets. None of the submitted models was judged to be satisfactory for four of the thirteen templates. 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.
+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" />. 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" />.
 ==See Also==