PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.791 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 1 PARENT 1VDR_A M 1 A 38 E 2 D 39 R 3 D 40 P 4 P 41 L 8 V 42 I 9 V 43 V 10 L 44 R 11 G 45 E 12 R 46 P 13 T 47 Y 14 T 48 A 15 F 49 S 16 E 50 L 17 S 51 I 18 M 52 V 19 R 53 D 20 D 54 R 33 D 55 H 34 L 56 R 35 P 57 G 36 G 58 P 37 S 59 L 38 A 60 G 39 Q 61 I 40 I 62 V 41 V 63 S 42 M 64 G 43 S 65 G 44 R 66 R 45 R 69 L 46 S 70 I 47 F 71 G 48 S 72 Q 49 V 73 A 50 D 74 D 51 T 75 L 52 A 76 V 53 H 77 G 54 R 78 V 55 A 79 E 56 A 80 G 57 S 81 V 61 V 82 E 62 E 83 E 63 E 84 L 64 A 85 L 65 V 86 A 66 D 87 H 67 I 88 Q 68 A 89 E 69 A 90 K 70 S 91 H 71 L 92 L 72 D 93 A 73 A 94 E 74 E 95 E 75 A 103 A 76 A 104 F 77 I 105 L 78 Y 106 R 79 A 107 A 80 L 108 Y 81 F 109 A 82 Q 110 K 83 P 111 D 84 H 112 E 85 D 114 P 86 R 115 L 87 M 116 Y 88 V 117 A 89 L 118 W 90 S 119 V 91 R 120 L 92 V 121 E 93 P 122 N 94 G 123 A 95 E 124 F 96 Y 125 R 97 E 126 Y 98 G 127 E 99 D 128 K 100 T 129 P 101 Y 130 L 102 Y 131 H 103 P 132 V 104 E 133 P 105 W 134 R 106 D 135 R 107 A 136 P 108 A 137 G 109 E 138 R 110 W 139 V 111 E 140 M 112 L 141 F 113 D 142 V 114 A 143 D 115 E 144 L 116 T 145 S 117 D 146 E 118 H 147 V 119 E 148 R 120 G 149 W 121 F 150 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.762 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 2 PARENT 1F9Z_A M 1 M 1 E 2 R 2 R 3 L 3 P 4 L 4 K 5 H 5 L 6 T 6 G 7 M 7 L 8 L 8 I 9 R 9 V 10 V 10 R 11 G 11 E 12 D 12 P 13 L 13 Y 14 S 16 A 15 I 17 S 16 D 18 L 17 F 19 I 18 Y 20 V 19 T 21 D 20 K 22 G 21 V 23 R 22 L 24 K 23 G 25 V 24 M 26 W 25 K 27 E 26 L 28 I 27 L 29 R 28 R 30 R 29 T 31 R 30 S 32 K 31 E 33 T 32 N 34 R 33 E 36 H 34 Y 37 R 35 K 38 G 36 Y 39 P 37 S 40 L 38 L 41 G 39 A 42 I 40 F 43 V 41 V 44 S 42 G 45 G 43 Y 46 G 44 G 47 R 45 P 48 L 46 E 49 I 47 T 50 G 48 E 51 Q 49 V 54 A 50 I 55 D 51 E 56 L 52 L 57 V 53 T 58 G 54 Y 59 V 55 N 60 E 56 W 61 G 57 G 62 P 58 V 63 F 59 L 77 S 60 S 78 V 61 V 79 E 62 D 80 L 72 N 81 A 73 A 82 E 74 A 83 E 75 E 84 A 76 A 85 F 77 C 86 L 78 E 87 R 79 K 88 A 80 I 89 Y 81 R 90 A 82 Q 91 K 83 N 92 D 84 G 93 E 85 G 94 P 86 N 95 L 87 V 96 Y 88 T 97 A 89 R 98 W 90 E 99 V 91 A 100 L 92 G 101 E 93 P 102 N 94 V 103 A 95 K 104 F 96 G 105 R 97 G 106 Y 98 T 107 E 99 T 108 K 100 V 109 P 101 I 110 L 102 A 111 H 103 F 112 V 104 V 113 P 105 E 114 R 106 D 115 R 107 P 116 P 108 D 117 G 109 G 118 R 110 K 120 V 111 I 121 M 112 E 122 F 113 L 123 V 114 I 124 D 115 E 125 L 116 E 126 S 117 G 127 E 118 N 128 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.762 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 3 PARENT 1C2N D 20 D 23 G 21 G 24 R 22 T 25 K 23 E 26 V 24 I 27 W 25 V 28 E 26 K 29 I 27 G 30 R 28 A 31 R 29 K 32 R 30 T 33 K 31 G 34 T 32 P 35 R 33 N 36 H 34 L 37 R 35 Y 38 G 36 G 39 S 42 V 40 G 43 V 41 G 44 G 42 R 45 R 43 L 46 T 44 I 47 A 45 G 48 G 46 Q 49 T 47 A 50 Y 48 D 51 P 49 E 56 E 50 G 57 F 51 P 58 K 52 F 59 Y 53 S 60 K 54 V 61 I 57 E 62 V 58 E 63 A 59 L 64 L 60 L 65 G 61 A 66 A 62 H 67 W 67 Q 68 T 68 E 69 E 69 K 70 E 70 H 71 D 71 L 72 I 72 A 73 A 73 E 74 T 74 E 75 Y 75 A 76 A 81 F 77 F 82 L 78 L 83 R 79 K 84 A 80 E 85 Y 81 K 86 A 82 L 87 K 83 D 88 D 84 D 89 E 85 K 90 R 97 K 91 Y 98 A 92 E 99 K 93 K 100 T 94 P 101 G 95 L 102 M 96 H 103 A 97 V 104 F 98 P 105 K 99 R 106 L 100 R 107 A 101 P 108 K 102 G 109 G 103 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.739 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 4 PARENT 1R9C_A M 1 E 3 E 2 G 4 R 3 L 5 P 4 S 6 K 5 H 7 L 6 M 8 G 7 T 9 L 8 F 10 I 9 I 11 V 10 V 12 R 11 R 13 E 12 D 14 P 13 R 20 Y 14 I 21 A 15 L 22 S 16 E 23 L 17 G 24 I 18 V 25 V 19 F 26 D 20 D 27 G 21 A 28 R 22 R 29 K 23 E 30 V 24 V 31 W 25 Y 32 E 26 A 33 I 27 S 34 R 28 D 35 R 29 T 36 R 30 E 37 K 31 Q 38 T 32 F 39 R 33 S 40 H 34 L 41 R 35 D 51 G 36 I 52 P 37 W 53 L 38 V 54 G 39 A 55 I 40 I 56 V 41 M 57 S 42 Q 58 G 43 G 59 G 44 E 60 R 45 K 61 L 46 L 62 I 47 A 63 G 48 E 64 Q 49 R 65 A 50 S 66 D 51 N 68 L 52 H 69 V 53 I 70 G 54 A 71 V 55 F 72 E 56 K 73 G 57 I 74 P 58 D 75 F 59 A 77 S 60 D 78 V 61 F 79 E 62 D 80 E 63 R 81 L 64 Y 82 L 65 A 83 A 66 E 84 H 67 R 85 Q 68 V 86 E 69 G 87 K 70 K 88 H 71 L 89 L 72 G 90 A 73 L 91 K 83 D 92 D 84 M 93 E 85 R 94 P 86 P 95 F 96 P 96 R 97 R 97 Y 98 P 98 E 99 G 99 K 100 R 100 P 101 S 101 L 102 I 102 H 103 Y 103 V 104 F 104 P 105 Y 105 R 106 D 106 R 107 D 107 P 108 D 108 G 109 N 109 R 110 H 110 V 111 M 111 M 112 F 112 F 113 E 113 V 114 L 114 D 115 H 115 L 116 T 116 S 117 G 117 E 118 T 118 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.723 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 5 PARENT 1NP6_A E 2 R 34 R 3 G 35 P 4 I 36 K 5 R 37 L 6 P 38 G 7 G 39 L 8 L 40 I 9 I 41 V 10 K 42 R 11 H 43 E 12 T 44 P 13 H 45 Y 14 H 46 A 15 E 47 S 16 L 48 L 17 R 49 I 18 K 50 V 19 A 51 D 20 G 52 G 21 A 53 R 22 Q 61 K 23 Q 62 V 24 R 63 W 25 W 64 E 26 A 65 I 27 L 66 R 28 M 67 R 29 T 68 R 30 E 69 K 31 T 70 T 32 P 71 R 33 D 72 H 34 S 88 R 35 K 89 G 36 L 90 P 37 D 91 L 38 L 92 G 39 I 93 I 40 L 94 V 41 V 95 S 42 E 96 G 43 G 97 G 44 F 98 R 45 K 99 L 46 H 100 I 47 E 101 G 48 E 102 Q 49 I 103 A 50 A 104 D 51 K 105 L 52 I 106 V 53 V 107 G 54 L 108 V 55 F 109 E 56 R 110 G 57 D 111 P 58 G 112 F 59 A 113 A 66 G 114 H 67 H 115 Q 68 R 116 E 69 P 117 K 70 E 118 H 71 E 119 L 72 L 120 A 73 V 121 K 83 I 122 D 84 D 123 E 85 R 124 P 86 H 125 L 87 V 126 Y 88 I 127 A 89 A 128 W 90 V 129 V 91 A 130 L 92 S 131 E 93 D 132 N 94 V 133 A 95 P 134 F 96 L 135 R 97 N 136 Y 98 L 137 E 99 D 138 K 100 V 139 L 102 A 140 H 103 L 141 V 104 L 142 P 105 D 143 R 106 I 144 R 107 N 145 P 108 D 146 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.703 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 6 PARENT 3DFR R 3 V 35 P 4 G 36 K 5 K 37 L 6 I 38 G 7 M 39 L 8 V 40 I 9 V 41 V 10 G 42 R 11 R 43 E 12 R 44 P 13 T 45 Y 14 Y 46 A 15 E 47 S 16 S 48 L 17 F 49 I 18 P 50 V 19 K 51 D 20 R 52 G 21 P 55 R 22 E 56 K 23 R 57 V 24 T 58 W 25 N 59 E 26 V 60 I 27 V 61 R 28 L 62 R 29 T 63 R 30 H 64 K 31 Q 65 T 32 E 66 R 33 D 67 H 34 Y 68 R 35 Q 69 G 36 A 70 P 37 Q 71 G 43 G 72 G 44 A 73 V 53 V 74 G 54 V 75 V 55 V 76 E 56 H 77 G 57 D 78 V 61 V 79 E 62 A 80 E 63 A 81 L 64 V 82 L 65 F 83 A 66 A 84 H 67 Y 85 Q 68 A 86 E 69 K 87 K 70 Q 88 H 71 H 89 L 72 L 90 A 73 D 91 E 74 Q 92 E 75 A 100 A 76 Q 101 F 77 I 102 L 78 F 103 R 79 T 104 A 80 A 105 Y 81 F 106 A 82 K 107 K 83 D 108 D 84 D 109 E 85 D 111 P 86 T 112 L 87 L 113 Y 88 L 114 A 89 V 115 W 90 T 116 V 91 R 117 L 92 L 118 E 93 A 119 N 94 G 120 A 95 S 121 F 96 F 122 R 97 E 123 Y 98 G 124 E 99 D 125 K 100 T 126 P 101 K 127 L 102 M 128 H 103 T 143 V 104 V 144 P 105 E 145 R 106 D 146 R 107 T 147 P 108 N 148 G 109 T 152 R 110 H 153 V 111 T 154 M 112 Y 155 F 113 E 156 V 114 V 157 D 115 W 158 L 116 Q 159 S 117 K 160 E 118 K 161 V 119 A 162 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.664 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 7 PARENT 1V62_A M 1 A 13 E 2 S 14 R 3 G 15 P 4 P 16 K 5 L 17 L 6 M 18 G 7 V 19 L 8 E 20 I 9 I 21 V 10 V 22 R 11 K 23 E 12 T 24 P 13 P 25 D 20 G 26 G 21 S 27 R 22 A 28 K 23 L 29 V 24 G 30 W 25 I 31 E 26 S 32 I 27 L 33 R 28 T 34 R 29 T 35 R 30 T 36 K 31 S 37 T 32 L 38 R 33 R 39 H 34 N 40 R 35 K 41 G 36 S 42 P 37 V 43 L 38 I 44 G 39 T 45 I 40 I 46 V 41 D 47 S 42 R 48 G 43 I 49 G 44 K 50 R 45 P 51 L 46 L 61 I 47 H 62 G 48 P 63 Q 49 G 64 A 50 D 65 D 51 H 66 L 52 I 67 V 53 L 68 G 54 S 69 V 55 I 70 E 56 D 71 G 57 G 72 F 59 T 73 S 60 S 74 V 61 M 75 E 62 E 76 H 71 H 77 L 72 C 78 A 73 S 79 E 74 L 80 E 75 L 81 A 76 E 82 F 77 A 83 L 78 T 84 R 79 K 85 A 80 L 86 Y 81 L 87 A 82 A 88 K 83 S 89 D 84 I 90 E 85 S 91 P 86 E 92 L 87 K 93 Y 88 V 94 A 89 R 95 W 90 L 96 V 91 E 97 L 92 I 98 E 93 L 99 N 94 P 100 A 95 V 101 F 96 P 102 R 97 Q 103 Y 98 S 104 E 99 Q 105 K 100 R 106 P 101 P 107 L 102 L 108 H 103 R 109 V 104 P 110 P 105 S 111 R 106 S 112 R 107 G 113 P 108 P 114 G 109 S 115 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.650 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 8 PARENT 1S1H_I P 4 P 19 K 5 S 20 L 6 V 21 G 7 Q 22 L 8 T 23 I 9 F 24 V 10 G 25 R 11 K 26 E 12 K 27 P 13 K 28 R 22 S 29 K 23 A 30 V 24 T 31 W 25 A 32 E 26 V 33 I 27 A 34 R 28 H 35 R 29 V 36 R 30 K 37 K 31 A 38 T 32 G 39 R 33 K 40 H 34 G 41 R 35 L 42 I 40 I 43 V 41 K 44 S 42 V 45 G 43 N 46 G 44 G 47 R 45 S 48 L 46 P 49 I 47 I 50 G 48 T 51 Q 49 I 77 A 50 D 78 D 51 I 79 L 52 R 80 V 53 V 81 G 54 R 82 V 55 V 83 E 56 T 84 G 57 G 85 P 58 G 86 F 59 G 87 S 60 H 88 V 61 V 89 E 62 S 90 E 63 Q 91 L 64 V 92 L 65 Y 93 A 66 A 94 H 67 I 95 Q 68 R 96 E 69 Q 97 K 70 A 98 H 71 I 99 E 75 A 100 A 76 K 101 F 77 G 102 L 78 L 103 R 79 V 104 A 80 A 105 Y 81 Y 106 A 82 H 107 K 83 Q 108 D 84 K 109 E 85 N 117 P 86 E 118 L 87 L 119 E 93 K 120 N 94 K 121 A 95 A 122 F 96 F 123 R 97 T 124 Y 98 Y 126 E 99 D 127 K 100 R 128 P 101 T 129 L 102 L 130 H 103 A 133 V 104 D 134 P 105 S 135 R 106 R 136 R 107 R 137 P 108 P 138 G 109 E 139 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.615 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 9 PARENT 1REG_X K 5 M 1 L 6 I 2 G 7 E 3 L 8 I 4 I 9 T 5 V 10 L 6 R 11 K 7 E 12 K 8 P 13 P 9 Y 14 K 14 A 15 V 15 S 16 K 16 L 17 E 17 I 18 T 18 V 19 L 19 D 20 T 20 G 21 R 21 W 25 M 22 E 26 G 23 I 27 I 24 R 28 A 25 R 29 N 26 R 30 N 27 K 31 K 28 T 32 D 29 R 33 K 30 G 39 V 31 I 40 L 32 V 41 Y 33 S 42 Q 34 G 43 S 35 G 44 C 36 R 45 H 37 L 46 I 38 I 47 L 39 G 48 Q 40 Q 49 K 41 A 50 K 42 D 51 G 43 L 52 L 44 V 53 Y 45 G 54 Y 46 V 55 I 47 F 59 V 48 S 60 H 49 V 61 F 50 E 62 K 51 E 63 E 52 L 64 M 53 L 65 L 54 A 66 R 55 H 67 M 56 Q 68 E 65 E 69 E 66 K 70 D 67 H 71 E 68 L 72 V 69 A 73 R 70 E 74 R 71 E 75 D 72 A 76 S 73 F 77 I 74 L 78 A 75 R 79 W 76 A 80 L 77 Y 81 L 78 A 82 E 79 K 83 D 80 D 84 W 81 E 85 G 82 P 86 L 83 L 87 I 84 W 90 E 85 V 91 I 86 L 92 V 87 E 93 P 88 N 94 G 89 A 95 Q 90 F 96 R 91 R 97 T 92 Y 98 F 93 E 99 M 94 K 100 K 95 P 101 D 96 L 102 L 97 H 103 R 102 V 104 V 103 P 105 I 104 R 106 S 105 R 107 F 106 P 108 K 107 G 109 Q 108 R 110 E 111 V 111 W 112 M 112 K 113 F 113 L 114 V 114 V 115 D 115 P 116 L 116 K 117 S 117 Y 118 E 118 T 119 V 119 I 120 R 120 G 121 W 121 N 122 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.590 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 10 PARENT 1S1I_M R 11 A 19 E 12 S 20 P 13 V 21 Y 14 V 22 A 15 A 23 S 16 K 24 L 17 Q 25 I 18 L 26 V 19 L 27 D 20 N 28 G 21 G 29 R 22 Q 30 K 23 K 31 V 24 I 32 W 25 V 33 E 26 V 34 I 27 V 35 R 28 R 36 R 29 A 37 R 30 E 38 K 31 E 39 T 32 L 40 R 33 N 41 H 34 I 42 R 35 S 43 G 36 G 44 S 42 E 45 G 43 F 46 G 44 F 47 R 45 R 48 L 46 L 57 I 47 R 58 G 48 K 59 Q 49 A 60 A 50 T 61 D 51 A 62 L 52 F 63 V 53 N 64 G 54 K 65 V 55 T 66 E 56 R 67 G 57 G 68 P 58 P 69 F 59 F 70 S 60 H 71 V 61 F 72 L 72 R 73 A 73 A 74 E 74 P 75 E 75 S 76 A 76 R 77 F 77 I 78 L 78 F 79 R 79 Y 80 A 80 K 81 Y 81 A 82 A 82 L 83 K 83 R 84 D 84 G 85 E 85 E 99 P 86 R 100 L 87 L 101 Y 88 K 102 A 89 V 103 W 90 F 104 V 91 E 105 L 92 G 106 E 93 I 107 N 94 P 108 A 95 P 109 R 97 P 110 Y 98 Y 111 E 99 D 112 K 100 K 113 P 101 K 114 L 102 K 115 H 103 R 116 V 104 V 117 P 105 V 118 R 106 V 119 R 107 P 120 P 108 Q 121 D 115 A 122 L 116 L 123 S 117 R 124 E 118 V 125 V 119 L 126 R 120 R 127 W 121 L 128 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.583 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 11 PARENT 1VKB_A R 3 H 3 P 4 H 4 K 5 M 5 L 6 A 6 G 7 H 7 L 8 I 8 I 9 F 9 V 10 V 10 R 11 Y 11 E 12 G 12 P 13 P 19 Y 14 N 20 A 15 H 21 S 16 K 22 L 17 V 23 I 18 M 24 V 19 L 25 D 20 D 26 G 21 G 30 R 22 L 31 K 23 A 32 V 24 A 33 W 25 F 34 E 26 R 35 I 27 G 36 R 28 R 37 R 29 G 38 R 30 C 39 K 31 T 40 T 32 V 41 R 33 E 42 P 37 S 43 L 38 F 44 G 39 P 45 I 40 L 46 V 41 V 47 S 42 I 48 G 43 A 49 G 44 G 50 R 45 E 51 L 46 H 65 I 47 C 66 G 48 V 67 Q 49 T 68 A 50 G 69 D 51 E 70 L 52 I 71 V 53 Y 72 G 54 E 73 V 55 V 74 E 56 D 75 E 62 E 76 E 63 Q 77 L 64 M 78 L 65 L 79 A 66 R 80 H 67 F 81 Q 68 L 82 E 69 D 83 K 70 D 84 H 71 F 85 L 72 E 86 D 84 D 87 E 85 C 88 P 86 P 89 E 93 S 90 N 94 M 91 A 95 Y 92 F 96 Q 93 R 97 R 94 Y 98 T 95 E 99 A 96 K 100 L 97 P 101 Q 98 L 102 V 99 H 103 Q 100 V 104 V 101 P 105 L 102 R 106 E 103 R 107 W 104 P 108 P 106 G 109 G 107 R 110 C 112 V 111 F 113 M 112 V 114 F 113 Y 115 V 114 T 116 D 115 T 117 L 116 A 118 S 117 T 119 E 118 Y 120 V 119 A 121 R 120 E 123 W 121 W 124 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.576 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 12 PARENT 1NKI_A M 1 T 3 E 2 G 4 R 3 L 5 P 4 N 6 K 5 H 7 L 6 L 8 G 7 T 9 L 8 L 10 I 9 A 11 V 10 V 12 R 11 A 13 E 12 D 14 P 13 L 15 Y 14 S 18 A 15 I 19 S 16 A 20 L 17 F 21 I 18 Y 22 V 19 R 23 D 20 D 24 G 21 L 26 R 22 G 27 K 23 F 28 V 24 R 29 W 25 L 30 E 26 E 31 I 27 A 32 R 28 R 33 R 29 W 34 R 30 D 35 K 31 Q 36 L 38 G 37 G 39 A 38 I 40 Y 39 V 41 L 40 S 42 E 41 G 43 L 42 G 44 G 43 R 45 S 44 L 46 L 45 D 51 W 46 L 52 L 47 V 53 C 48 G 54 L 49 V 55 S 50 E 56 R 51 G 57 E 52 P 58 P 53 F 59 I 69 S 60 A 70 V 61 A 71 E 62 A 72 E 63 D 73 L 64 F 74 L 65 A 75 A 66 R 76 H 67 F 77 Q 68 A 78 E 69 A 79 K 70 Q 80 L 78 L 81 R 79 R 82 A 80 A 83 Y 81 H 84 A 82 G 85 K 83 V 86 D 84 R 87 V 91 E 88 L 92 W 89 E 93 K 90 N 94 Q 91 A 95 N 92 F 96 R 93 R 97 S 94 Y 98 E 95 E 99 G 96 K 100 D 97 P 101 S 98 L 102 F 99 H 103 Y 100 V 104 F 101 P 105 L 102 R 106 D 103 R 107 P 104 P 108 D 105 G 109 G 106 R 110 H 107 V 111 R 108 M 112 L 109 F 113 E 110 V 114 A 111 D 115 H 112 L 116 V 113 S 117 G 114 E 118 D 115 V 119 L 116 R 120 R 117 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.574 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 13 PARENT 1GEF_A Y 14 L 12 A 15 I 13 S 16 K 14 L 17 L 15 I 18 L 16 V 19 E 17 D 20 K 18 G 21 H 19 R 22 G 20 W 25 F 21 E 26 A 22 I 27 V 23 R 28 V 24 R 29 R 25 R 30 S 26 K 31 A 27 T 32 G 28 R 33 S 29 H 34 K 30 R 35 K 31 G 36 V 32 P 37 D 33 L 38 L 34 G 39 V 35 I 40 A 36 V 41 G 37 S 42 N 38 G 43 G 39 G 44 K 40 R 45 K 41 L 46 Y 42 I 47 L 43 G 48 C 44 Q 49 I 45 A 50 E 46 D 51 V 47 L 52 K 48 V 53 V 49 G 54 T 50 V 55 K 51 E 56 K 52 G 57 D 53 P 58 H 54 F 59 L 55 S 60 D 61 V 61 M 62 E 62 G 63 E 63 R 64 L 64 L 65 L 65 I 66 A 66 E 67 H 67 F 68 Q 68 S 69 E 69 R 70 K 70 R 71 H 71 F 72 L 72 G 73 A 73 G 74 E 85 I 75 P 86 P 76 L 87 V 77 Y 88 L 78 A 89 A 79 W 90 V 80 V 91 K 81 L 92 F 82 E 93 L 83 N 94 N 84 A 95 V 92 F 96 S 93 R 97 P 94 Y 98 K 95 E 99 I 96 K 100 E 97 P 101 K 98 L 102 F 99 H 103 V 100 V 104 F 101 P 105 T 102 R 106 P 103 R 107 S 104 P 108 S 105 G 109 G 106 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.555 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 14 PARENT 1LBA R 30 A 1 K 31 K 2 T 32 Q 3 R 33 R 4 H 34 E 5 R 35 S 6 G 36 T 7 P 37 D 8 L 38 A 9 G 39 I 10 I 40 F 11 V 41 V 12 S 42 H 13 G 43 C 14 G 44 S 15 R 45 A 16 L 46 T 17 I 47 K 18 G 48 P 19 E 56 S 20 G 57 Q 21 P 58 N 22 F 59 V 23 S 60 G 24 V 61 V 25 E 62 R 26 E 63 E 27 L 64 I 28 L 65 R 29 A 66 Q 30 H 67 W 31 Q 68 H 32 E 69 K 33 K 70 E 34 H 71 Q 35 L 72 G 36 K 83 W 37 D 84 L 38 E 85 D 39 P 86 V 40 L 87 G 41 Y 88 Y 42 A 89 H 43 W 90 F 44 V 91 I 45 L 92 I 46 E 93 K 47 N 94 R 48 A 95 D 49 F 96 G 50 R 97 T 51 Y 98 V 52 E 99 E 53 K 100 A 54 P 101 G 55 L 102 M 59 H 103 A 60 V 104 V 61 P 105 G 62 R 106 S 63 R 107 H 64 P 108 H 70 G 109 N 71 R 110 S 72 V 111 I 73 M 112 G 74 F 113 V 75 V 114 C 76 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.545 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 15 PARENT 1N13_B R 22 V 73 K 23 P 74 V 24 T 75 W 25 A 76 E 26 Y 77 I 27 G 78 R 28 Y 79 R 29 I 80 R 30 I 81 K 31 S 82 T 32 D 83 R 33 V 84 H 34 P 85 R 35 G 86 G 36 E 87 P 37 T 88 L 38 I 89 G 39 S 90 I 40 A 91 V 41 A 92 S 42 I 93 G 43 S 94 G 44 V 95 R 45 A 96 L 46 I 97 I 47 P 98 G 48 K 99 Q 49 C 104 A 50 G 105 D 51 L 106 L 52 I 107 V 53 M 108 G 54 E 109 V 55 Y 110 E 56 E 111 G 57 G 112 P 58 K 113 F 59 C 114 S 60 S 115 V 61 K 116 E 62 K 117 E 63 E 118 L 64 A 119 L 65 E 120 A 66 K 121 H 67 T 122 Q 68 V 123 E 69 R 124 K 70 E 125 H 71 M 126 E 74 A 127 E 75 K 128 A 76 I 129 F 77 G 130 L 78 F 131 R 79 E 132 A 80 M 133 Y 81 R 134 A 82 G 135 K 83 W 136 D 84 E 137 E 85 L 138 P 86 D 139 L 87 R 140 Y 88 I 141 A 89 E 142 W 90 S 143 V 91 I 144 L 92 A 145 E 93 V 146 N 94 E 147 H 103 H 148 V 104 T 149 P 105 V 150 R 106 E 151 R 107 K 152 P 108 L 153 G 109 G 154 R 110 C 155 V 111 A 156 M 112 F 157 F 113 A 158 V 114 A 159 D 115 A 160 L 116 A 161 S 117 L 162 E 118 W 163 V 119 Y 164 R 120 K 165 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.533 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 16 PARENT 1LQ9_A M 1 V 4 E 2 N 5 R 3 D 6 P 4 P 7 K 5 R 8 L 6 V 9 G 7 G 10 L 8 F 11 I 9 V 12 V 10 A 13 R 11 V 14 E 12 V 15 P 13 T 16 Y 14 L 28 A 15 V 29 S 16 E 30 L 17 L 31 I 18 A 32 V 19 T 33 D 20 G 34 G 21 G 35 R 22 V 36 K 23 Q 37 V 24 F 46 W 25 L 47 E 26 S 48 I 27 A 49 R 28 T 50 R 29 Y 51 R 30 H 52 K 31 A 53 T 32 S 54 R 33 T 55 H 34 D 56 G 44 G 57 R 45 T 58 L 46 A 59 Q 49 V 60 A 50 V 61 D 51 N 62 L 52 Y 63 V 53 A 64 G 54 Q 65 V 55 W 66 E 56 E 67 G 57 S 68 L 65 E 69 A 66 Q 70 H 67 A 71 Q 68 Y 72 E 69 R 73 K 70 V 74 H 71 N 75 L 72 F 76 A 73 G 77 E 74 R 81 E 75 S 82 A 76 A 83 F 77 E 84 L 78 L 85 R 79 R 86 A 80 E 87 Y 81 A 88 A 82 L 89 K 83 S 90 D 84 S 91 E 85 L 92 P 86 P 93 N 94 G 94 A 95 L 95 F 96 M 96 R 97 G 97 Y 98 P 98 E 99 P 99 K 100 K 100 P 101 A 101 L 102 V 102 H 103 F 103 V 104 M 104 P 105 T 105 R 106 P 106 R 107 R 107 P 108 G 108 G 109 A 109 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.532 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 17 PARENT 1CXC M 1 N 13 E 2 Q 14 R 3 C 15 P 4 Q 16 K 5 T 17 L 6 C 18 G 7 H 19 L 8 V 20 I 9 I 21 V 10 V 22 R 11 D 23 E 12 D 24 D 20 S 25 G 21 G 26 R 22 T 27 E 26 T 28 I 27 I 29 R 28 A 30 R 29 G 31 R 30 R 32 K 31 N 33 T 32 A 34 R 33 K 35 H 34 T 36 R 35 G 37 G 36 P 38 P 37 N 39 L 38 L 40 G 39 Y 41 I 40 G 42 V 41 V 43 S 42 V 44 G 43 G 45 G 44 R 46 R 45 T 47 L 46 A 48 I 47 G 49 G 48 T 50 Q 49 Q 51 A 50 A 52 D 51 D 53 L 52 F 54 V 53 K 55 G 54 G 56 V 55 Y 57 G 57 G 58 P 58 A 70 F 59 W 71 S 60 D 72 V 61 E 73 E 62 E 74 E 63 H 75 L 64 F 76 L 65 V 77 A 66 Q 78 H 67 Y 79 Q 68 V 80 E 69 Q 81 K 70 D 82 H 71 P 83 E 75 T 84 A 76 K 85 F 77 F 86 L 78 L 87 R 79 K 88 A 80 E 89 Y 81 Y 90 A 82 T 91 K 83 G 92 D 84 D 93 E 85 A 94 P 86 K 95 L 87 A 96 Y 88 K 97 A 89 G 98 E 93 K 99 N 94 M 100 A 95 T 101 F 96 F 102 R 97 K 103 Y 98 L 104 E 99 K 105 K 100 K 106 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.523 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 18 PARENT 1COT M 1 F 12 E 2 N 13 R 3 K 14 P 4 C 15 K 5 K 16 L 6 A 17 G 7 C 18 L 8 H 19 I 9 M 20 V 10 I 21 R 11 Q 22 E 12 A 23 P 13 P 24 D 20 D 25 G 21 G 26 R 22 T 27 K 23 D 28 V 24 I 29 W 25 I 30 E 26 K 31 I 27 G 32 R 28 G 33 R 29 K 34 R 30 T 35 K 31 G 36 T 32 P 37 R 33 N 38 H 34 L 39 R 35 Y 40 G 36 G 41 S 42 V 42 G 43 V 43 G 44 G 44 R 45 R 45 L 46 K 46 I 47 I 47 G 48 A 48 Q 49 S 49 A 50 E 50 E 56 E 51 G 57 G 52 P 58 F 53 F 59 K 54 S 60 Y 55 V 61 G 56 E 62 E 57 E 63 G 58 L 64 I 59 L 65 L 60 A 66 E 61 H 67 V 62 Q 68 A 63 E 69 E 64 K 70 K 65 H 71 N 66 L 72 P 67 A 73 D 82 E 74 P 83 E 75 K 84 A 76 P 85 F 77 W 86 L 78 L 87 R 79 V 88 A 80 K 89 Y 81 M 90 A 82 T 91 K 83 D 92 D 84 D 93 E 85 K 94 P 86 G 95 L 87 A 96 Y 88 K 97 A 89 T 98 E 93 K 99 N 94 M 100 A 95 T 101 F 96 F 102 R 97 K 103 Y 98 M 104 E 99 G 105 K 100 K 106 P 101 N 107 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.514 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 19 PARENT 1IHK_A R 3 R 69 P 4 T 70 K 5 G 71 L 6 F 72 G 7 H 73 L 8 L 74 I 9 E 75 V 10 I 76 R 11 F 77 E 12 P 78 D 20 N 79 G 21 G 80 R 22 T 81 W 25 I 82 E 26 Q 83 I 27 G 84 R 28 T 85 R 29 R 86 R 30 K 87 K 31 D 88 T 32 H 89 R 33 S 90 H 34 R 91 R 35 F 92 G 36 G 93 P 37 I 94 L 38 L 95 G 39 E 96 I 40 F 97 V 41 I 98 S 42 S 99 R 45 I 100 L 46 A 101 I 47 V 102 G 48 G 103 Q 49 L 104 A 50 V 105 D 51 S 106 L 52 I 107 V 53 R 108 G 54 G 109 V 55 V 110 E 56 D 111 G 57 S 112 P 86 G 113 L 87 L 114 Y 88 Y 115 A 89 L 116 W 90 G 117 V 91 M 118 L 92 N 119 E 93 E 120 N 94 K 121 A 95 G 122 F 96 Y 125 R 97 G 126 Y 98 S 127 E 99 E 128 K 100 K 129 P 101 L 130 L 102 T 131 H 103 Q 139 V 104 F 140 P 105 E 141 R 106 E 142 R 107 N 143 P 108 W 144 G 109 Y 145 R 110 N 146 V 111 T 147 M 112 Y 148 F 113 S 149 V 114 S 150 D 115 N 151 L 116 L 152 S 117 Y 153 E 118 K 154 V 119 H 155 R 120 V 156 W 121 D 157 TER END PFRMAT AL TARGET t0227 AUTHOR LOOPP SCORE 0.507 REMARK CONFIDENCE NONE REMARK LOOPP v3.0 with LOOPP driver v3.1 [ALI] (08/24/04 12:18 EST) (compiled Sep 20 2004 17:13:12) REMARK prediction finished on Mon Oct 11 09:03:25 2004 EST METHOD Automated LOOPP protein structure prediction server. METHOD http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm METHOD LOOPP is a fold recognition program based on the collection METHOD of numerous signals, merging them into a single score, and METHOD generating atomic coordinates based on an alignment into a METHOD homologue template structure. The signals we are using include METHOD straightforward sequence alignment, sequence profile, threading, METHOD secondary structure and exposed surface area prediction. METHOD (Secondary structure and exposed surface prediction program (sable) METHOD was developed in the group of our collaborator Professor Jaroslaw METHOD Meller). These individual signals are combined locally to create METHOD mixed models and globally to provide overall scores. Computations METHOD of scores to those that can be done quickly are performed for all METHOD proteins in our database and expensive scores (such as Z score METHOD calculations) are computed only for those that score highly with the METHOD 'cheap' score. Atomic models are then generated using an alignment METHOD produced by the scoring scheme and the Modeller program of Andrej Sali. METHOD The final atomic structure is evaluated by additional energy scores. METHOD The energies used, and the combination of individual scores are METHOD determined by a Mathematical Programming algorithm. MODEL 20 PARENT 1FIT R 3 K 11 P 4 P 12 K 5 S 13 L 6 V 14 G 7 V 15 L 8 F 16 I 9 L 17 V 10 K 18 R 11 T 19 E 12 E 20 K 23 L 21 V 24 S 22 W 25 F 23 E 26 A 24 I 27 L 25 R 28 V 26 R 29 N 27 R 30 R 28 K 31 K 29 T 32 P 30 R 33 V 31 H 34 V 32 R 35 P 33 G 36 G 34 P 37 H 35 L 38 V 36 G 39 L 37 I 40 V 38 V 41 C 39 S 42 P 40 G 43 L 41 G 44 R 42 G 54 P 43 V 55 V 44 E 56 E 45 G 57 R 46 P 58 F 47 F 59 H 48 S 60 D 49 V 61 V 55 E 62 A 56 E 63 D 57 L 64 L 58 L 65 F 59 A 66 Q 60 H 67 T 61 Q 68 T 62 E 69 Q 63 K 70 R 64 H 71 V 65 E 75 G 66 A 76 T 67 F 77 V 68 L 78 V 69 R 79 E 70 A 80 K 71 Y 81 H 72 A 82 F 73 K 83 H 74 D 84 G 75 E 85 T 76 W 90 S 77 V 91 L 78 L 92 T 79 E 93 F 80 N 94 S 81 A 95 Q 82 F 96 D 83 R 97 G 84 Y 98 P 85 E 99 E 86 K 100 A 87 P 101 G 88 L 102 Q 89 H 103 T 90 V 104 V 91 P 105 K 92 R 106 H 93 R 107 V 94 P 108 H 95 G 109 V 96 R 110 H 97 V 111 V 98 M 112 L 99 F 113 P 100 V 114 R 101 D 115 K 102 L 116 A 103 S 117 G 104 E 118 D 105 V 119 A 106 R 120 S 107 W 121 W 108 TER END