CASP3 Target Difficulty

Click on targets in the image to jump to the corresponding table entry below. This is a graph plotting two measures of similarity between CASP3 targets and structure neighbors as defined by VAST. The fraction superimposed by VAST is the fraction of the CASP3 target protein that has been used for structure superpositions to VAST neighbors. %Sequence ID in structure alignment gives the agreement between the sequences in the structure (sequence independent) superpositions as calculated by VAST. The values are averages across those templates/VAST-neighbors aligning at least 85% of the length of the most extensive alignment found. Targets plotted in blue are from CASP2, and the averages for these have been generated from the original structure comparison results used for CASP2.

Prediction problems plotted with a "x"-symbol have characteristic sequence motifs that allow for recognition of the correct fold by motif matching and profile-based sequence comparisons. Open circles indicate problems for which VAST has identified similar structures, and filled circles indicate cases where VAST neighbors, if any, conserve less than 25% of intra-molecular non-local contacts in structure superpositions (averaged as explained above).

Predicted correctly? On this "phase diagram" of target difficulty, square boxes around the plotting symbols indicate targets for which at least one prediction team has submitted models crossing a threshold of model accuracy and fold recognition specificity. At least 20% of the "bet" must have been placed on a correct fold, and at least 50% of the corresponding model must be aligned correctly (allowing for a small local shift error). One may draw a line, it seems, between prediction problems that can be solved by todays threading methods and those that can't, as demonstrated above.

CASP3 Threading Target Table

Follow the links in the table below to display additional information about Fold-Recognition problems at CASP3.

Target	Name	Nres	Exp	PDB	Pb	Description
T0043	HPPK	158	Xray	1HKA	+	7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase
T0044	RTCA	347	Xray	1QMH	-	RNA-3'terminal phosphate cyclase
T0046	ADG	119	Xray	-	-	Gamma-Adaptin ear domain
T0052	CV-N	101	NMR	2EZM	+	Cyanovirin-N
T0053	CBIK	264	Xray	1QGO	+	CbiK protein
T0054	VANX	202	Xray	-	+	VanX protein
T0056	DNAB	114	NMR	1JWE	+	DnaB helicase N-terminal domain
T0059	SMD3	75	Xray	1D3B	+	Sm D3 protein, N-terminal 75 residues
T0061	HDEA	89	Xray	1BG8	+	Protein HDEA
T0063	IF5A	138	Xray	1BKB	+	Translation initiation factor 5A
T0067	PBP	187	Xray	1BD9	+	Phosphatidylethanolamine Binding Protein
T0071	ADAC	238	Xray	1B9K	+	Alpha adaptin, ear domain
T0075	ETS-1	110	NMR	1BQV	+	Ets-1 protein fragment
T0077	L30	105	NMR	1CK2	+	Ribosomal protein L30
T0079	MARA	129	Xray	1BL0	+	MarA protein
T0080	3MG	219	Xray	1BNK	+	3-methyladenine DNA glycosylase
T0081	MGSA	152	Xray	1B93	+	Methylglyoxal synthase
T0083	CYNS	156	Xray	1DW9	+	Cyanase