PFRMAT AL 
TARGET T0083 
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         SEQUENCE AND ITS HOMOLOGS: 
METHOD                     In addition to the target sequence we use  
METHOD                     sequences homologous to the target one as identified 
METHOD                     by gaped BLAST. Then matrix of interactions is 
METHOD                     averaged over these sequences and used for threading. 
METHOD                     If Bij_m is the energy of interaction between residues  
METHOD                     in positions i and j of the m-th sequences, then 
METHOD                           Bij=<Bij_m> 
METHOD                      is the average matrix of interactions. 
METHOD 
METHOD		   REF: Mirny,L.A. 
METHOD			"From Lattice Model to Real Proteins" 
METHOD			Ph.D.Thesis, Harvard University 1998  
METHOD 
METHOD			Mirny,L.A. Finkelstein,A.V. and Shakhnovich E.I. 
METHOD			"Protein Structure Prediction with the Aid of Homologous Sequences" 
METHOD		        in preparation for Proteins 
METHOD 
METHOD 
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         SEQUENCE-STRUCTURE ALIGNMENT: 
METHOD                    Final sequence-structure alignment is done for 20 top  
METHOD                    scoring template using a Monte Carlo threading. In Monte Carlo  
METHOD                    threading gaps are allowed at any position of sequence or structure. 
METHOD			  Gaps are not penalized, instead a fragment of continuous matches is  
METHOD                    constrained to be longer than 5 residues. The optimal alignment is 
METHOD                    obtained by simulated 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 1eny 
 Q   5 A   2  
 I   6 G   3  
 N   7 L   4  
 R   8 L   5  
 N   9 D   6  
 I  10 G   7  
 R  11 K   8  
 L  12 R   9  
 D  13 I  10  
 L  14 L  11  
 I  18 V  12  
 L  19 S  13  
 L  20 G  14  
 S  21 I  15  
 K  22 I  16  
 A  23 T  17  
 K  25 D  18  
 D  26 S  19  
 L  27 S  20  
 S  28 I  21  
 F  29 A  22  
 A  30 F  23  
 E  31 I  25  
 I  32 A  26  
 A  33 R  27  
 D  34 V  28  
 G  35 A  29  
 T  36 Q  30  
 G  37 E  31  
 L  38 Q  32  
 A  39 G  33  
 E  40 A  34  
 A  41 Q  35  
 F  42 L  36  
 V  43 V  37  
 A  46 L  38  
 L  47 T  39  
 L  48 G  40  
 G  49 F  41  
 Q  50 D  42  
 Q  51 R  43  
 A  52 L  44  
 L  53 R  45  
 P  54 L  46  
 A  55 I  47  
 D  56 Q  48  
 A  57 I  50  
 A  58 T  51  
 R  59 D  52  
 L  60 R  53  
 V  61 L  54  
 G  62 P  55  
 A  63 A  56  
 K  64 K  57  
 L  65 A  58  
 D  66 P  59  
 L  67 L  60  
 S  71 L  61  
 I  72 E  62  
 L  73 L  63  
 L  74 D  64  
 L  75 V  65  
 Q  76 Q  66  
 M  77 L  71  
 I  78 A  72  
 P  79 S  73  
 L  80 L  74  
 R  81 A  75  
 G  82 G  76  
 C  83 R  77  
 I  84 V  78  
 D  85 T  79  
 D  86 E  80  
 R  87 A  81  
 I  88 I  82  
 P  89 G  83  
 T  90 A  84  
 D  91 G  85  
 P  92 N  86  
 T  93 K  87  
 M  94 L  88  
 Y  95 D  89  
 R  96 G  90  
 F  97 V  91  
 Y  98 V  92  
 E  99 H  93  
 M 100 S  94  
 L 101 I  95  
 Q 102 G  96  
 V 103 H 121  
 Y 104 I 122  
 G 105 S 123  
 T 106 A 124  
 T 107 Y 125  
 L 108 S 126  
 K 109 Y 127  
 A 110 A 128  
 L 111 S 129  
 V 112 M 130  
 H 113 A 131  
 E 114 K 132  
 K 115 A 133  
 F 116 L 134  
 G 117 L 135  
 D 118 P 136  
 G 119 I 137  
 I 120 M 138  
 I 121 N 139  
 S 122 P 140  
 A 123 G 141  
 I 124 G 142  
 N 125 S 143  
 F 126 I 144  
 K 127 V 145  
 L 128 G 146  
 D 129 V 171  
 V 130 N 172  
 K 131 R 173  
 K 132 F 174  
 V 133 V 175  
 A 134 A 176  
 D 135 E 178  
 P 136 A 179  
 E 137 G 180  
 G 138 K 181  
 G 139 Y 182  
 E 140 G 183  
 R 141 V 184  
 A 142 R 185  
 V 143 S 186  
 I 144 N 187  
 T 145 L 188  
 L 146 V 189  
 D 147 A 239  
 G 148 K 240  
 K 149 T 241  
 Y 150 V 242  
 L 151 C 243  
 P 152 A 244  
 T 153 L 245  
 K 154 L 246  
 P 155 S 247  
 F 156 D 248  
TER 
END 
