%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % B-factor and local structure quality estimation % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1. How was the local quality estimated? The local quality was defined as the distance deviation (in Angstrom) between residue positions in the model and the native structure. It was estimated using support vector regression that makes use of the local structural between the model and (1) threading templates, (2) structure alignment templates, (3) reference decoys, and (4) sequence-based secondary structure and solvent accessibility predictions. Large-scale benchmark tests show that the estimated local quality has an average error of 1.4 Angstrom and AUC score of 0.89 for well-predicted I-TASSER models. Based on these tests, the local quality estimations tend to be more accurate for residues: 1) that have higher threading alignment coverage 2) that are located at alpha-helix and beta-strand regions 3) that are buried (at 25% threshold) The estimated local quality for the model is available at the columns 68-74 in the model's PDB file and also at the bottom of this page (the column with label RSQ_3). 2. What is B-factor? The B-factors can be taken as indicating the stability of different parts of the structure. Atoms with low B-factors are well-ordered and those with high B-factors are very flexible. Normalized B-factor for a target protein is defined as z-score-based normalization of the raw B-factor values. The normalized B-factor (called B-factor profile, BFP) is predicted using a combination of both template-based assignment and profile-based prediction. Based on the distributions and predictions of the BFP, residues with BFP values higher than 0 are less stable in experimental structures. The BFP is converted back to B-factor by inverse z-score-based transformation. The B-factor for the model is available at the columns 61-66 in the model's PDB file. Both normalized at and raw B-factors are available at the bottom of this page (the columns with labels nBF and rBF). 3. How were the TM-score and RMSD estimated? TM-score and RMSD are known standards for measuring the structural similarity between two structures which are usually used to measure the accuracy of structure modeling when the native structure is known. In case where the native structure is unknown, it becomes necessary to predict the quality of the modeling prediction, i.e. what is the distance between the model and its native structure? To answer this question, we tried to predict the TM-score and RMSD of the model relative to its native structure based on the predicted local distances, with the corresponding TM-score and RMSD formula. For more information about the local quality and B-factor predictions, please refer to the following article: Jianyi Yang and Yang Zhang, ResQ: A unified algorithm for estimating B-factor and residue-specific quality of protein structure prediction, submitted, (2014). Estimated TM-score: 0.91 Estimated RMSD: 1.58 Angstrom Estimated local quality and B-factor: #RES SS SA COV nBF rBF RSQ_1 RSQ_2 RSQ_3 RSQ_4 1 C E 0.25 2.00 40.83 14.76 10.24 7.31 6.92 2 C E 0.29 1.42 36.05 9.76 13.60 4.91 4.65 3 C E 0.30 0.91 31.93 5.38 11.48 3.54 3.50 4 C B 0.33 0.47 28.33 2.34 2.06 1.81 1.74 5 C E 0.35 0.64 29.73 3.53 6.03 2.51 2.43 6 C E 0.42 0.91 31.91 9.06 9.59 2.91 2.57 7 C E 0.46 0.78 30.86 9.77 9.88 3.26 2.80 8 C E 0.45 0.33 27.16 11.52 9.95 3.11 2.58 9 C B 0.51 0.25 26.53 9.92 9.48 2.44 1.87 10 C E 0.85 0.52 28.68 5.16 4.46 1.49 1.19 11 C E 0.96 0.50 28.53 2.47 2.55 1.68 1.50 12 C E 0.96 0.12 25.49 0.98 1.55 1.39 1.23 13 S B 1.00 -0.17 23.11 0.67 0.65 0.92 0.92 14 S E 1.00 -0.37 21.44 0.84 0.81 0.74 0.74 15 S B 1.00 -0.52 20.26 0.59 0.70 0.70 0.73 16 S B 1.00 -0.57 19.81 0.41 0.45 0.61 0.63 17 S B 1.00 -0.56 19.87 0.54 0.59 0.93 0.97 18 C B 1.00 -0.40 21.21 0.51 0.47 0.73 0.64 19 C B 1.00 -0.35 21.65 0.63 0.57 0.76 0.65 20 C B 1.00 -0.19 22.93 0.90 0.86 0.77 0.56 21 C B 1.00 -0.01 24.38 0.72 0.83 0.82 0.67 22 C E 0.99 0.42 27.94 1.94 1.93 1.40 1.24 23 C E 0.99 0.74 30.50 2.39 2.47 1.91 1.76 24 C E 1.00 0.49 28.44 4.26 3.36 1.68 1.35 25 C E 1.00 0.48 28.37 3.29 3.07 1.23 0.97 26 C E 1.00 0.43 27.96 0.92 0.72 0.91 0.83 27 C E 1.00 0.22 26.25 0.73 0.65 0.90 0.76 28 C B 1.00 -0.07 23.92 0.97 0.87 1.12 1.01 29 S B 0.99 -0.40 21.24 1.19 1.16 1.03 1.01 30 S B 0.99 -0.55 20.02 0.94 0.90 0.85 0.87 31 S B 0.99 -0.60 19.59 1.11 0.98 0.65 0.63 32 S B 0.99 -0.62 19.45 0.70 0.56 0.85 0.86 33 S B 0.99 -0.54 20.05 0.79 0.78 0.78 0.80 34 S B 0.99 -0.49 20.48 1.27 1.01 0.61 0.58 35 S B 0.99 -0.25 22.43 1.47 1.69 0.98 0.76 36 S E 0.99 0.16 25.81 1.89 3.02 1.32 1.17 37 C E 0.99 0.41 27.84 6.13 2.68 2.02 1.68 38 C E 0.99 0.33 27.20 2.58 2.42 1.77 1.66 39 S E 0.99 0.03 24.74 1.41 1.56 1.33 1.27 40 S E 0.99 -0.02 24.29 1.66 1.36 1.67 1.58 41 S E 0.99 -0.02 24.32 1.32 1.67 1.06 1.04 42 S E 0.99 -0.05 24.07 1.66 1.48 1.43 1.34 43 C E 0.99 0.13 25.52 1.13 1.07 1.08 1.01 44 C E 0.99 0.12 25.43 0.89 1.16 1.11 1.01 45 C E 0.99 0.41 27.86 1.33 1.67 1.11 1.02 46 C E 0.99 0.58 29.21 2.25 2.34 2.34 2.29 47 C B 1.00 0.15 25.70 1.54 1.56 1.33 1.20 48 C B 1.00 0.20 26.09 0.67 0.77 1.08 1.01 49 H B 1.00 0.13 25.57 1.05 1.13 1.18 1.09 50 H B 1.00 0.03 24.73 0.86 0.84 0.97 0.90 51 H E 1.00 -0.18 23.03 0.87 0.78 1.05 0.97 52 H E 1.00 -0.34 21.70 0.53 0.52 0.76 0.63 53 H B 1.00 -0.37 21.49 0.56 0.46 0.71 0.62 54 H B 1.00 -0.41 21.14 0.53 0.64 0.74 0.66 55 H E 1.00 -0.40 21.24 0.54 0.61 0.73 0.60 56 H B 1.00 -0.49 20.48 0.70 0.60 0.73 0.65 57 H B 1.00 -0.47 20.62 0.61 0.74 0.79 0.72 58 H B 1.00 -0.41 21.12 0.73 0.79 0.92 0.78 59 H E 1.00 -0.32 21.83 0.74 0.76 0.94 0.84 60 H B 1.00 -0.33 21.82 0.81 0.88 1.09 0.99 61 H B 1.00 -0.23 22.61 2.04 1.98 1.49 1.39 62 H E 1.00 0.14 25.58 2.72 2.83 2.66 2.46 63 C E 1.00 0.37 27.51 2.03 1.93 1.44 1.23 64 C E 1.00 0.54 28.86 3.82 2.10 2.10 1.84 65 C E 1.00 0.46 28.20 2.44 2.29 1.64 1.52 66 C B 1.00 0.14 25.62 2.14 2.03 1.35 1.21 67 S E 1.00 0.05 24.86 1.51 1.27 0.90 0.76 68 S B 1.00 -0.30 22.02 1.00 0.89 0.57 0.56 69 S E 1.00 -0.39 21.25 1.15 1.02 0.90 0.90 70 S B 1.00 -0.50 20.40 0.87 0.83 0.78 0.79 71 S B 1.00 -0.55 19.95 0.81 0.71 0.53 0.52 72 S B 1.00 -0.52 20.20 0.70 0.66 0.74 0.76 73 C B 1.00 -0.26 22.33 0.95 0.83 1.09 0.99 74 H B 1.00 -0.39 21.27 0.96 0.95 1.35 1.24 75 H E 0.99 -0.08 23.80 1.36 1.37 1.15 1.00 76 H B 1.00 -0.19 22.91 1.52 1.69 1.32 1.18 77 H B 1.00 -0.25 22.44 1.32 1.03 1.15 1.07 78 H B 1.00 -0.05 24.10 1.39 1.18 0.84 0.71 79 C E 0.99 0.00 24.49 1.77 2.00 1.21 1.00 80 C B 0.95 -0.07 23.88 1.83 1.78 1.08 0.93 81 C B 0.95 0.05 24.87 1.92 1.70 1.30 1.15 82 C E 0.93 0.22 26.25 2.27 2.19 1.32 1.09 83 C E 0.91 0.34 27.27 2.51 2.10 1.28 1.06 84 C B 0.88 0.28 26.74 3.20 1.73 1.28 0.95 85 C B 0.76 0.02 24.64 2.64 1.82 1.06 0.84 86 H E 0.75 0.28 26.78 2.50 2.11 1.20 1.06 87 H E 0.76 0.32 27.07 3.02 2.01 1.43 1.28 88 H B 0.72 0.12 25.43 3.40 1.52 1.28 1.06 89 H E 0.74 0.50 28.54 4.01 1.71 1.43 1.15 90 C E 0.75 1.00 32.60 4.52 1.73 1.82 1.52 91 C E 0.72 0.65 29.77 3.02 1.60 1.97 1.77 92 C E 0.78 0.45 28.14 2.87 2.09 1.64 1.49 93 C B 0.88 0.27 26.65 1.79 2.03 1.41 1.34 94 C E 0.90 0.18 25.94 4.07 3.79 1.49 1.27 95 C E 0.88 0.23 26.34 1.71 1.91 1.04 0.96 96 C E 0.96 0.42 27.86 2.92 2.42 1.74 1.53 97 C E 0.97 0.19 26.03 1.43 0.94 1.28 1.19 98 H E 0.96 0.17 25.87 0.97 0.97 1.14 1.01 99 H E 1.00 0.25 26.48 0.85 0.78 1.39 1.30 100 H B 1.00 -0.15 23.24 0.76 0.63 0.90 0.82 101 H B 1.00 -0.23 22.56 0.82 0.66 0.89 0.81 102 H E 0.99 -0.06 24.02 0.75 0.66 0.93 0.83 103 H E 1.00 -0.03 24.23 0.80 0.65 1.07 0.99 104 H B 0.89 -0.26 22.36 0.75 0.77 1.07 1.01 105 H B 1.00 -0.17 23.08 0.89 0.99 0.90 0.80 106 H E 0.99 0.13 25.55 1.11 1.02 1.01 0.91 107 H E 1.00 0.01 24.56 1.27 1.04 1.18 1.03 108 H B 1.00 -0.02 24.33 1.37 1.24 1.18 1.09 109 H B 0.93 0.28 26.79 1.44 1.34 1.60 1.47 110 C E 0.85 0.51 28.67 1.92 1.71 1.81 1.69 111 C E 0.88 0.45 28.11 1.62 2.03 2.21 2.17 112 C E 0.96 0.26 26.58 2.15 2.50 1.51 1.31 113 C E 1.00 0.09 25.20 0.80 0.87 0.94 0.82 114 S B 1.00 -0.25 22.42 0.99 1.02 0.72 0.70 115 S E 1.00 -0.22 22.67 1.06 1.09 0.98 0.94 116 S B 1.00 -0.37 21.42 1.10 0.90 0.97 0.94 117 S E 0.99 -0.36 21.51 0.84 0.85 0.88 0.89 118 S B 1.00 -0.31 21.95 0.86 0.94 0.76 0.72 119 S B 1.00 -0.11 23.56 0.86 1.01 0.94 0.81 120 C E 0.91 0.15 25.68 1.92 2.46 1.05 0.90 121 C B 0.95 0.31 27.04 2.20 2.14 1.07 0.89 122 C B 0.93 0.61 29.45 2.28 2.75 1.11 0.88 123 C E 0.90 0.89 31.70 2.99 3.10 1.44 1.19 124 C E 0.99 1.08 33.29 4.34 4.39 1.39 1.14 125 C E 0.99 0.71 30.24 2.25 2.36 1.06 0.91 126 C E 0.99 0.36 27.40 1.09 1.14 1.05 0.91 127 C E 0.99 0.14 25.64 0.93 0.80 1.16 0.99 128 H B 0.99 -0.01 24.40 0.98 0.99 0.77 0.68 129 H E 0.99 0.30 26.94 1.34 1.23 1.08 0.93 130 H E 0.99 0.10 25.28 1.13 0.99 1.07 0.95 131 H B 0.99 -0.24 22.52 0.75 0.78 0.80 0.72 132 H B 0.99 -0.22 22.70 1.10 1.08 1.11 0.94 133 H E 0.99 -0.02 24.30 1.05 0.92 0.96 0.83 134 H B 0.99 -0.28 22.21 0.67 0.66 0.71 0.63 135 H B 0.99 -0.32 21.85 0.70 0.81 0.69 0.61 136 H E 0.97 -0.15 23.29 1.40 1.27 1.04 0.90 137 H E 0.97 -0.00 24.44 1.66 1.25 1.14 0.97 138 H B 0.94 -0.14 23.31 2.59 1.44 1.08 0.86 139 H B 0.93 -0.11 23.55 1.95 1.53 1.11 0.95 140 H E 0.86 0.55 28.97 3.54 2.22 1.47 1.23 141 H E 0.82 0.85 31.41 5.03 1.76 1.56 1.20 142 H E 0.75 1.29 35.00 6.30 2.29 1.59 1.18 143 C E 0.57 1.98 40.66 8.45 5.78 4.99 4.77 RES: Residue number SS: Predicted secondary structure: C - random coil; H - alpha-helix; S - beta-strand RSA: Predicted solvent accessibility at 25% cutoff: E - exposed; B - buried COV: Threading alignment coverage defined as the number of non-gap threading alignments on the residue divided by the total number of threading templates nBF: Predicted normalized B-factor (normalize by Z-score transformation) rBF: Predicted raw B-factor RSQ_1: Predicted local quality based on LOMETS threading templates RSQ_2: Predicted local quality based on TM-align structure alignment templates RSQ_3: Consensus prediction of local quality based on support vector regressions RSQ_4: Predicted local quality based on submitted decoy structures You are requested to cite the following article when you use the ResQ server: Jianyi Yang and Yang zhang, ResQ: A unified algorithm for estimating B-factor and residue-specific quality of protein structure prediction, submitted, (2014).