| Literature DB >> 21931639 |
Sandhya Agarwal1, Nitish Kumar Mishra, Harinder Singh, Gajendra P S Raghava.
Abstract
BACKGROUND: Mannose binding proteins (MBPs) play a vital role in several biological functions such as defense mechanisms. These proteins bind to mannose on the surface of a wide range of pathogens and help in eliminating these pathogens from our body. Thus, it is important to identify mannose interacting residues (MIRs) in order to understand mechanism of recognition of pathogens by MBPs.Entities:
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Year: 2011 PMID: 21931639 PMCID: PMC3172211 DOI: 10.1371/journal.pone.0024039
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Figure 1Schematic diagram of pathway of mannose binding lectins, recognition of mannose on pathogens and process of phagocytosis.
Figure 2Schematic representation of algorithm used to generate patterns from a given protein sequences and their binary and composition profile.
Figure 3Comparison of percent amino acid composition of mannose interacting and non-interacting residues.
Figure 4Comparison of percent composition of MIRs and Non-MIRs based on properties of residues.
Figure 5Two Sample logo graph between MIRs and Non-MIRs patterns.
Figure 6Overall amino acids comparison of MIRs and Non-MIRs patterns.
The performance of SVM models developed on main dataset (Window length 17) using binary, evolutionary and compositional profile (complete table shown in Table S1).
| Binary | PSSM | Composition | ||||||||||
| Thes | Sen | Spe | Acc | MCC | Sen | Spe | Acc | MCC | Sen | Spe | Acc | MCC |
| −0.3 | 81.21 | 30.34 | 55.77 | 0.13 | 85.6 | 36.76 | 61.18 | 0.26 | 96.77 | 41.64 | 69.21 | 0.46 |
| −0.2 | 73.44 | 39.43 | 56.44 | 0.14 | 82.58 | 43.91 | 63.24 | 0.29 | 93.84 | 48.39 | 71.11 | 0.47 |
| −0.1 | 66.09 | 49.44 | 57.76 | 0.16 | 78.05 | 50.15 | 64.1 | 0.29 | 87 | 66.47 | 76.74 | 0.55 |
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| 73.51 | 57.8 | 65.66 | 0.32 |
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| 0.1 | 49.74 | 68.54 | 59.14 | 0.19 |
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| 68.82 | 90.13 | 79.47 | 0.60 |
| 0.2 | 40.65 | 75.89 | 58.27 | 0.18 | 59.01 | 68.68 | 63.85 | 0.28 | 63.44 | 94.62 | 79.03 | 0.61 |
| 0.3 | 31.56 | 82.89 | 57.2 | 0.17 | 51.56 | 73.82 | 62.69 | 0.26 | 56.79 | 96.48 | 76.64 | 0.58 |
*Bold values indicate the point where sensitivity and specificity is equal or minimum difference with maximum MCC.
The performance of composition based SVM model developed on main dataset using window length 21, 23 and 25 (complete tables shown in Tables S2 & S3).
| 21 Window | 23 Window | 25 Window | ||||||||||
| Thes | Sen | Spe | Acc | MCC | Sen | Spe | Acc | MCC | Sen | Spe | Acc | MCC |
| −0.3 | 91.55 | 50.53 | 71.04 | 0.46 | 96.60 | 41.59 | 69.10 | 0.46 | 96.31 | 37.03 | 66.67 | 0.41 |
| −0.2 | 86.69 | 70.46 | 78.57 | 0.58 | 93.78 | 55.00 | 74.39 | 0.53 | 93.68 | 48.59 | 71.14 | 0.47 |
| −0.1 | 83.87 | 82.02 | 82.94 | 0.66 | 89.99 | 72.89 | 81.44 | 0.64 | 90.48 | 66.67 | 78.57 | 0.59 |
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| 86.78 | 82.80 | 84.79 | 0.70 | 87.17 | 77.07 | 82.12 | 0.65 |
| 0.1 | 75.90 | 92.52 | 84.21 | 0.69 |
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| 84.94 | 83.87 | 84.40 | 0.69 |
| 0.2 | 71.53 | 94.66 | 83.09 | 0.68 | 80.37 | 92.91 | 86.64 | 0.74 |
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| 0.3 | 65.99 | 95.92 | 80.95 | 0.65 | 76.48 | 94.85 | 85.67 | 0.73 | 77.45 | 91.93 | 84.69 | 0.70 |
Bold values indicate the point where sensitivity and specificity is equal or minimum difference with maximum MCC.
The performance of composition based SVM model developed on realistic dataset using different window lengths (complete data in Table S4).
| Window Lengths | Thes | Sen | Spe | Acc | MCC |
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| −0.7 | 75.61 | 91.07 | 89.66 | 0.54 |
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| −0.7 | 76.68 | 90.48 | 89.22 | 0.53 |
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| −0.7 | 77.75 | 90.52 | 89.36 | 0.54 |
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| −0.7 | 80.27 | 89.89 | 89.02 | 0.54 |
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| −0.7 | 69.39 | 94.37 | 92.10 | 0.58 |
The performance of composition based SVM models in term of AUC on realistic dataset.
| Window Lengths | SVM parameter | AUC |
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| g:0.01 c:2 j:2 | 0.855 |
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| g:0.01 c:1 j:2 | 0.868 |
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| g:0.01 c:1 j:2 | 0.869 |
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| g:0.01 c:1 j:2 | 0.863 |
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| g:0.01 c:1 j:1 | 0.894 |
*SVM parameters, RBF kernal (g), trade-off between training error & margin (c), cost-factor (j).
Figure 7ROC plot for composition based SVM modules at different windows length.