GOAL

The goal of LSD-CAFASP is to evaluate the accuracy of loops and side-chains in protein structure prediction. An additional goal is to assess the capabilities of the tools to generate models whose structures are closer to the corresponding native structure than to the templates used.

TEST SET

A number of prediction targets will be selected from PDB-CAFASP. PDB-CAFASP gathers structure predictions from automatic fold-recognition servers using as targets those pre-release PDB entries, with no significant sequence similarity to proteins already in the PDB.

Those PDB-CAFASP targets for which a highly reliable structure prediction is observed (e.g. many of the fully-automated servers report similar results with above-threshold scores) will be selected for LSD-CAFASP. As has been demonstrated in CAFASP3, the highly reliable FR alignments provided by the servers are relatively accurate, and thus, can be used the basis for loop and side-chain modeling.

In LSD-CAFASP the alignments and the templates will be supplied so that all participants start their modeling using the exact same data.

After the native structures of each target is obtained, we will evaluate how accurate the selected FR alignment was. If the selected FR alignment contains regions which significantly differ from the native structure, so that a meaningful evaluation of the LSD-CAFASP predictions can not be carried out, then these regions/loops will be excluded form the evaluation.

CURRENT TARGETS :

Target	LSD-CAFASP submission deadline (IDT)	Sequence-Template Alignment From Server	Predicted backbone model
1MOI	9-Mar-2003	fugue3.0 ali , pdb-model
1MQW	17-Mar-2003	inbgu.0 ali , pdb-model
1MRZ	19-Mar-2003	3dpsm.1 ali, pdb-model
1MZK	08-Apr-2003	orfeus.0
1N8N	21-May-2003	inbgu.0
1NE2	10-Jun-2003	fugue3.2
1J2G	05-Jul-2003	inbgu.0 ali , pdb-model
1NTE	29-Jul-2003	ffa3.0

EXPIRED TARGETS :

Target	LSD-CAFASP submission deadline (IDT)	Sequence-Template Alignment From Server	Accuracy of the selected pdb-model (MaxSub)	MaxSub superposition of selected pdb-model and native
1MWM	Expired	fugue3.0 ali , pdb-model (NOTE: partial match)	12.7 A RMSD; MaxSub score: 2.8 (subset: 106/312 at 1.7 A RMSD)
1M33	Expired	fugue3.5 ali , pdb-model	2.9 A RMSD; MaxSub score: 6.2 (subset: 197/266 at 1.7 A RMSD)
1MKE	Expired	ffas3.1 ali , pdb-model	3.3 A RMSD; MaxSub score: 5.2 (subset: 94/144 at 2.8 A RMSD)
1KYT	Expired	fugue3.2 ali , pdb-model (NOTE: partial match)	19.6 A RMSD; MaxSub score: 2.6 (subset: 67/210 at 1.5 A RMSD)

DEADLINES

The targets will be available for prediction until the specified deadline or until their 3D structure are released. Targets will expire also if the structure of a homologous protein is released. Predictions should be submitted to dfischer@cs.bgu.ac.il in PDB format only and will be accepted anytime before the expiration time.

Upon release of the experimental structure, the predictions will be compared and assessed.

To ensure that the predictions were made using the sequence-template alignment provided by LSD-CAFASP, each prediction will be checked to see if at least 90% of their C-alphas of the core are identical to the those of structure implied by the provided alignment. Predictions that will differ by more than 10% will be disqualified from the main LSD-CAFASP evaluation, and will be evaluated in a special "different source" category.

ORGANIZING COMMITTEE:

Daniel Fischer dfischer@cs.bgu.ac.il.

Leszek Rychlewski