PFRMAT SS 
TARGET T0077 
AUTHOR 3707-4066-9021 
REMARK PROBABILITIES ESTIMATED FROM A CONFIDENCE SCALE 
METHOD SIMPA with homologues.  
METHOD SIMPA is a nearest neighbour method for predicting secondary  
METHOD      structures using a similarity matrix, in its latest version 
METHOD      the Blossum 62, an optimized similarity threshold , a window of 
METHOD      13 to 17 residues and a database of observed secondary structures. 
METHOD      In version simpa96 used here, the database contains circa 300 
METHOD      proteins and the window is 13 residues. Its crossvalidated accuracy 
METHOD      was a Q3 of 67.7% for a single sequence and 72.8% when using 
METHOD      multiple alignments of homologues sequences. 
METHOD       
METHOD      J. LEVIN, B. ROBSON, J. GARNIER. An Algorithm for secondary 
METHOD      structure determination in proteins based on sequence similarity. 
METHOD      FEBS, 205, (1986) 303-308. 
METHOD       
METHOD      J. LEVIN, J. GARNIER. Improvements in a secondary structure 
METHOD      prediction method based on a search for local sequence homologies 
METHOD      and its use as a model building tool. Biochim. Biophys. Acta,  
METHOD      (1988)  955, 283-295. 
METHOD       
METHOD      J. LEVIN. Exploring the limits of nearest neighbour secondary 
METHOD      structure prediction. Protein Eng. (1997),7, 771-776 
MODEL 1 
 M C 0.10 
 A C 0.10 
 P C 0.10 
 V H 0.10 
 K H 0.01 
 S H 0.01 
 Q H 0.10 
 E H 0.10 
 S H 0.20 
 I H 0.30 
 N H 0.10 
 Q H 0.10 
 K H 0.30 
 L H 0.20 
 A E 0.10 
 L E 0.01 
 V E 0.01 
 I E 0.01 
 K C 0.20 
 S C 0.50 
 G C 0.60 
 K C 0.40 
 Y E 0.10 
 T E 0.20 
 L E 0.10 
 G C 0.20 
 Y H 0.20 
 K H 0.01 
 S H 0.10 
 T H 0.20 
 V H 0.30 
 K H 0.30 
 S H 0.30 
 L H 0.30 
 R H 0.10 
 Q C 0.10 
 G C 0.40 
 K C 0.40 
 S C 0.40 
 K E 0.01 
 L E 0.40 
 I E 0.50 
 I E 0.50 
 I E 0.50 
 A E 0.10 
 A C 0.40 
 N C 0.60 
 T C 0.60 
 P C 0.40 
 V C 0.20 
 L C 0.01 
 R H 0.01 
 K H 0.10 
 S H 0.01 
 E H 0.01 
 L H 0.30 
 E H 0.30 
 Y H 0.30 
 Y H 0.30 
 A H 0.20 
 M H 0.20 
 L H 0.10 
 S C 0.01 
 K C 0.10 
 T C 0.20 
 K C 0.30 
 V E 0.01 
 Y E 0.10 
 Y E 0.10 
 F C 0.10 
 Q C 0.40 
 G C 0.60 
 G C 0.60 
 N C 0.30 
 N C 0.10 
 E E 0.01 
 L E 0.01 
 G C 0.10 
 T C 0.10 
 A C 0.01 
 V C 0.10 
 G C 0.20 
 K C 0.20 
 L C 0.01 
 F C 0.10 
 R E 0.01 
 V E 0.01 
 G E 0.10 
 V E 0.30 
 V E 0.40 
 S E 0.40 
 I E 0.30 
 L E 0.01 
 E C 0.40 
 A C 0.60 
 G C 0.70 
 D C 0.60 
 S C 0.40 
 D E 0.20 
 I E 0.10 
 L E 0.10 
 T E 0.01 
 T E 0.01 
 L C 0.01 
 A C 0.10 
 END 
