PFRMAT AL 
TARGET T0045 
AUTHOR 7072-5255-2426 
METHOD 
METHOD         POTENTIAL:  
METHOD                    A contact pairwise potential is obtained 
METHOD                    by optimization procedure which minimizes 
METHOD                    Zscores in the training set. The Z-score 
METHOD                    of a sequence-structure pair is computed with 
METHOD                    respect to random compact conformations. 
METHOD 
METHOD               REF: L. Mirny and E. Shakhnovich                   
METHOD                    "How to determine protein folding potential?  
METHOD                     A new approach to the old problem." 
METHOD                     J.Mol.Biol. 1996, v264, p1164-1169 
METHOD 
METHOD         FOLD RECOGNITION: 
METHOD                    Fast threading is done by complete enumeration 
METHOD                    of alignments with no more than one gap. Structures 
METHOD                    that provide the lowest Z-scores are subject of 
METHOD                    the final alignment. No frozen approximation! No gap penalties! 
METHOD			  (to be published) 
METHOD 
METHOD         FINAL ALIGNMENT: 
METHOD                    Final sequence-structure alignment is done for 20 top  
METHOD                    scoring structures using Monte Carlo search in  
METHOD                    the space of alignments. Optimization is done by simulated  
METHOD                    annealing. 
METHOD 
METHOD                    Different quantitative measures (Z-score, 
METHOD                    transition heat capacity Cv, alignment entropy) are used  
METHOD                    to assess the quality of final alignment 
METHOD 
METHOD                REF: Mirny, L.A. and Shakhnovich, E.I. 
METHOD                     Fold Recognition by Threading: Why it Works, Why it Doesn't  
METHOD                     J.Mol.Biol. to appear in v282 1998 
METHOD  
METHOD  
METHOD  
MODEL  1 
PARENT 1gyp_A 
 M   1 I   7  
 T   2 N   8  
 P   3 G   9  
 A   4 F  10  
 I   5 G  11  
 D   6 R  12  
 L   7 I  13  
 L   8 G  14  
 K   9 R  15  
 K  10 M  16  
 Q  11 V  17  
 K  12 F  18  
 I  13 Y 106  
 P  14 V 107  
 F  15 I 108  
 I  16 E 109  
 L  17 S 110  
 H  18 T 111  
 T  19 G 112  
 Y  20 F 114  
 D  21 T 115  
 H  22 D 116  
 D  23 K 117  
 P  24 L 118  
 N  25 K 119  
 N  26 A 120  
 Q  27 E 121  
 H  28 G 122  
 F  29 H 123  
 G  30 I 124  
 D  31 K 125  
 E  32 G 126  
 A  33 G 127  
 A  34 A 128  
 E  35 K 129  
 K  36 K 130  
 L  37 V 131  
 G  38 V 132  
 I  39 I 133  
 D  40 S 134  
 P  41 A 135  
 N  42 P 136  
 R  43 A 137  
 S  44 S 138  
 F  45 A 141  
 K  46 K 142  
 T  47 T 143  
 L  48 I 144  
 L  49 V 145  
 V  50 M 146  
 A  51 G 147  
 E  52 V 148  
 N  53 N 149  
 G  54 Q 150  
 D  55 H 151  
 Q  56 E 152  
 K  57 Y 153  
 K  58 H 158  
 L  59 H 159  
 A  60 V 160  
 C  61 V 161  
 F  62 S 162  
 V  63 N 163  
 L  64 A 164  
 A  65 S 165  
 T  66 C 166  
 A  67 T 167  
 N  68 T 168  
 M  69 N 169  
 L  70 C 170  
 N  71 L 171  
 L  72 A 172  
 K  73 P 173  
 K  74 I 174  
 A  75 V 175  
 A  76 H 176  
 K  77 G 188  
 S  78 L 189  
 I  79 M 190  
 G  80 T 191  
 V  81 T 192  
 K  82 I 193  
 V  84 H 194  
 E  85 S 195  
 M  86 Y 196  
 A  87 T 197  
 D  88 A 198  
 K  89 T 199  
 D  90 Q 200  
 A  91 N 220  
 A  92 I 221  
 Q  93 I 222  
 K  94 P 223  
 S  95 S 224  
 T  96 T 225  
 G  97 T 226  
 Y  98 G 227  
 L  99 A 228  
 V 100 A 229  
 G 101 K 230  
 G 102 A 231  
 I 103 V 232  
 S 104 G 233  
 P 105 M 234  
 L 106 V 235  
 G 107 I 236  
 Q 108 P 237  
 K 109 L 243  
 K 110 T 244  
 R 111 G 245  
 V 112 M 246  
 K 113 S 247  
 T 114 F 248  
 V 115 R 249  
 I 116 V 250  
 K 117 D 254  
 S 118 V 255  
 T 119 S 256  
 A 120 V 257  
 L 121 V 258  
 E 122 D 259  
 F 123 L 260  
 E 124 T 261  
 T 125 R 306  
 I 126 S 307  
 Y 127 S 308  
 V 128 V 309  
 S 129 Y 310  
 G 130 D 311  
 G 131 F 327  
 K 132 K 328  
 R 133 V 329  
 G 134 V 330  
 L 135 S 331  
 S 136 W 332  
 V 137 Y 333  
 E 138 D 334  
 I 139 N 335  
 A 140 E 336  
 P 141 W 337  
 Q 142 A 338  
 L 144 Y 339  
 A 145 S 340  
 K 146 H 341  
 V 147 R 342  
 L 148 V 343  
 G 149 V 344  
 A 150 D 345  
 F 152 L 346  
 T 153 V 347  
 D 154 R 348  
 I 155 Y 349  
 V 156 M 350  
 D 157 A 351  
 E 158 A 352  
TER 
END 
