Critical Assessment of Fully Automated Structure Prediction



The goal of PDB-CAFASP, like CAFASP3 and LiveBench, is to evaluate the performance of fully automatic 3D protein structure prediction servers. The difference in PDB-CAFASP is the set of targets on which it is applied. CAFASP uses CASP targets, LiveBench uses newly released pdb entries, while PDB-CAFASP uses as targets pre-release PDB entries. Pre-release PDB entries are entries soon to be released, whose structures are not yet published, but whose sequence is known. PDB-CAFASP thus increases the size of the test set on which the servers are evaluated.

PDB-CAFASP will take place at the end of 2002. All CAFASP participants are invited to participate in PDB-CAFASP3. Further details will be announced in this site.


A server's developer willing to include his/her server in PDB-CAFASP3 needs to register by sending an email to Participation in PDB-CAFASP3 is independent of LiveBench, CAFASP and CASP. New servers that did not enter CAFASP3, can enter PDB-CAFASP3, and conversely, CAFASP3 servers may wish not to participate in PDB-CAFASP3. For PDB-CAFASP3 there will be no parallel registration to CASP.


Pre-release pdb entries will be submitted at a rate of ca. one per day. Submission will be like in CAFASP3.

As the raw servers' output of the registered servers is collected, it will be made available to all, in the PDB-CAFASP3 web-site. This will allow anybody to use the predictions from the automated servers for any purpose. Participation in PDB-CAFASP3 explicitly implies that the developer agrees that his/her server's results will be published and used by others.


The evaluation in PDB-CAFASP3 will be identical to that applied in LiveBench. As the 3D structure of each target is released, the automatic evaluation will be updated and will be available to all at all times.

Note: EVA is another structure prediction experiment, devised by B. Rost, which is also based on pre-released pdb entries. Because the set of targets used, the participating servers and the evaluation procedures applied are not identical, EVA and PDB-CAFASP provide complementary and valuable assessments.


If you want to enquire about PDB-CAFASP3, email us: or