Epitope Prediction Based on Random Peptide Library Screening: Benchmark Dataset and Prediction Tools Evaluation
Abstract
:1. Introduction
2. Results and Discussion
2.1. Datasets Compilation
2.2. Performance Evaluation for the Existing Epitope Prediction Software
Method | Publication year | Language | Operating System | Service | Notes |
---|---|---|---|---|---|
FINDMAP | 2003 | C++ | not stated | no | FINDMAP is a method to acquire information on the 3D structure of the protein by identifying discontinuous epitopes; it maps one mimotope sequence to the protein at a time. |
SiteLight | 2005 | C++ | Linux | no | SiteLight is a method of predicting the binding site on a 3D structure using random peptide library screening. |
3DEX | 2005 | VB | Windows | no | 3DEX allows the analysis of single amino acid of a linear peptide sequence with regard to their spatial neighborhood in the 3D structures of PDB files based on preselectable parameters like distance, string length (frame size) and surface exposure. It maps mimotopes to the protein one by one, one sequence at a time. |
MIMOP | 2006 | PHP | Independent | Upon request | MIMOP provides an environment for mimotope characterization which integrates two main approaches, MimAlign and MimCons, which deliver to the user mimotope analysis results. |
MIMOX | 2006 | Perl | Independent | Web | MIMOX has two sections, the first is to derive the consensus sequence, and the second is to map the single sequence to the target protein. |
Mapitope | 2007 | C++ | Windows | Web | Mapitope is based on that epitope determinants shared by the entire set of peptides are detected. Both web service and source code is available. |
PepSurf | 2007 | C++ | Linux | Web | PepSurf is an algorithm for mapping a set of affinity-selected peptides to the solved surface of the antigen. Both web service and source code is available. |
Pepitope | 2007 | C++ | Windows | Web | Pepitope is a combination algorithm of PepSurf and Mapitope, the web service is available freely on the Pepitope server. |
MEPS | 2007 | Java | Independent | Web | MEPS provides two services, one is to evaluate the likelihood that a given peptide to mimic exposed regions of the protein, and the other one is to generate all peptides of a given length to mimic exposed regions of the protein. |
Pep-3D-Search | 2008 | VB | Windows | Graphic interface | Pep-3D-Search is an epitope mapping algorithm based on both mimotope and motif analysis. The source code is available freely. |
EpiSearch | 2009 | not stated | not stated | Web | EpiSearch is an automated detection of conformational epitopes using random peptide library screening. It provides web service freely. |
2.2.1. Criteria and datasets used in methods evaluation
2.2.2. Evaluation through MCC
MimoID | Antigen | ALL | Mapitope | PepSurf | Pepitope | Pep-3D-Search | EpiSearch | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
MCC | PPV | MCC | PPV | MCC | PPV | MCC | PPV | MCC | PPV | |||||
Antigen-Antibody | ||||||||||||||
MS00012* | 2OSL_P | 25 | NA | NA | 0.182 | 0.250 | NA | NA | 0.145 | 0.200 | 0.190 | 0.267 | ||
MS00013* | 3IU3_I | 223 | 0.146 | 0.667 | 0.045 | 0.231 | 0.071 | 0.500 | 0.168 | 0.471 | 0.134 | 0.500 | ||
MS00029* | 1TET_P | 15 | 0.564 | 1.000 | 0.617 | 1.000 | 0.564 | 1.000 | 0.510 | 0.900 | 0.856 | 1.000 | ||
MS00030 | 1TET_P | 15 | 0.471 | 1.000 | 0.679 | 1.000 | 0.471 | 1.000 | NA | NA | NA | NA | ||
MS00048* | 1YY9_A | 624 | -0.066 | 0.000 | -0.003 | 0.000 | -0.033 | 0.000 | 0.049 | 0.400 | -0.005 | 0.000 | ||
MS00049* | 1N8Z_C | 607 | 0.100 | 0.692 | 0.059 | 0.455 | 0.041 | 1.000 | 0.114 | 0.500 | 0.096 | 0.48 | ||
MS00052 | 2ADF_A | 196 | 0.074 | 0.429 | 0.164 | 0.556 | —— | —— | 0.157 | 0.359 | NA | NA | ||
MS00053* | 2ADF_A | 196 | -0.015 | 0.000 | 0.032 | 0.167 | -0.010 | 0.000 | 0.189 | 0.889 | 0.106 | 0.500 | ||
MS00054* | 1IQD_C | 156 | 0.093 | 0.142 | -0.006 | 0.091 | 0.113 | 1.000 | 0.023 | 0.130 | 0.129 | 0.360 | ||
MS00055* | 2GHW_A | 203 | 0.100 | 0.400 | 0.029 | 0.208 | —— | —— | -0.082 | 0.000 | 0.080 | 0.320 | ||
MS00056 | 2GHW_A | 203 | 0.110 | 0.444 | 0.110 | 0.385 | —— | —— | -0.089 | 0.000 | —— | —— | ||
MS00057 | 2NY7_G | 317 | 0.004 | 0.100 | 0.026 | 0.222 | —— | —— | 0.006 | 0.097 | 0.062 | 0.300 | ||
MS00058 | 2NY7_G | 317 | -0.015 | 0.000 | —— | —— | —— | —— | 0.000 | 0.083 | —— | —— | ||
MS00059* | 2NY7_G | 317 | 0.152 | 0.560 | 0.052 | 0.205 | 0.088 | 0.556 | 0.001 | 0.086 | 0.085 | 0.333 | ||
MS00099 | 1N8Z_C | 607 | 0.076 | 0.600 | -0.066 | 0.000 | NA | NA | -0.005 | 0.000 | 0.005 | 0.059 | ||
MS00185* | 1G9M_G | 321 | 0.102 | 0.324 | 0.063 | 0.226 | 0.091 | 0.412 | -0.001 | 0.044 | -0.015 | 0.000 | ||
MS00186* | 1E6J_P | 210 | 0.021 | 0.167 | 0.158 | 0.478 | 0.036 | 0.333 | 0.119 | 0.275 | 0.114 | 0.364 | ||
MS00242 | 2OSL_P | 25 | NA | NA | 0.145 | 0.200 | NA | NA | 0.145 | 0.200 | NA | NA | ||
Protein-Protein | ||||||||||||||
MS00041* | 1OC0_B | 51 | 0.226 | 0.364 | 0.166 | 0.375 | 0.166 | 0.375 | 0.101 | 0.310 | 0.254 | 0.440 | ||
MS00047* | 1HX1_B | 114 | 0.028 | 0.238 | 0.114 | 0.360 | —— | —— | -0.022 | 0.167 | 0.190 | 0.480 | ||
MS00060* | 1WLP_B | 138 | -0.073 | 0.000 | -0.033 | 0.160 | -0.040 | 0.000 | 0.065 | 0.279 | —— | —— | ||
MS00062* | 1WLP_A | 25 | 0.496 | 0.789 | 0.180 | 0.714 | 0.499 | 1.000 | NA | NA | 0.530 | 1.000 | ||
MS00139* | 1K4U_S | 62 | 0.247 | 0.778 | 0.217 | 1.000 | 0.247 | 0.778 | 0.391 | 0.611 | —— | —— | ||
MS00276 | 2GRX_A | 725 | -0.007 | 0.000 | 0.041 | 0.261 | -0.006 | 0.000 | -0.006 | 0.026 | 0.004 | 0.069 | ||
MS00277* | 2GRX_A | 725 | -0.007 | 0.000 | 0.039 | 0.429 | -0.006 | 0.000 | 0.006 | 0.071 | 0.029 | 0.222 | ||
MS00278 | 2GSK_A | 590 | -0.008 | 0.000 | 0.070 | 0.545 | -0.003 | 0.000 | 0.038 | 0.263 | -0.018 | 0.000 | ||
MS00279* | 2GSK_A | 590 | 0.033 | 0.184 | 0.047 | 0.400 | 0.047 | 0.400 | -0.011 | 0.000 | -0.016 | 0.000 | ||
MS00357* | 1FLT_X | 95 | 0.228 | 0.727 | 0.140 | 0.750 | 0.140 | 0.750 | 0.005 | 0.227 | 0.259 | 0.688 | ||
MS00384* | 3DOW_B | 12 | 0.527 | 1.000 | 0.764 | 1.000 | 0.527 | 1.000 | NA | NA | NA | NA | ||
MS00405* | 1SHY_A | 234 | 0.008 | 0.125 | 0.036 | 0.200 | 0.017 | 0.200 | -0.005 | 0.088 | -0.020 | 0.045 | ||
MS00464 | 1SQ0_A | 214 | 0.077 | 0.444 | 0.021 | 0.188 | NA | NA | 0.037 | 0.194 | 0.080 | 0.333 | ||
MS00465* | 1SQ0_A | 214 | -0.029 | 0.000 | 0.002 | 0.133 | -0.025 | 0.000 | 0.046 | 0.231 | 0.071 | 0.357 | ||
MS00671* | 1D4V_B | 163 | -0.046 | 0.000 | 0.117 | 0.381 | -0.021 | 0.000 | -0.039 | 0.000 | -0.017 | 0.083 | ||
MS00976* | 3BT1_A | 135 | 0.240 | 0.786 | -0.073 | 0.114 | —— | —— | 0.240 | 0.593 | 0.025 | 0.240 | ||
MS00984* | 1EER_A | 166 | 0.078 | 0.455 | 0.006 | 0.250 | -0.033 | 0.000 | 0.089 | 0.500 | 0.001 | 0.231 | ||
MS01004 | 1MQ8_B | 177 | -0.031 | 0.000 | -0.030 | 0.000 | NA | NA | -0.014 | 0.069 | NA | NA | ||
MS01036* | 3EZE_B | 85 | 0.071 | 0.400 | 0.331 | 0.917 | 0.230 | 0.857 | 0.393 | 0.850 | 0.313 | 0.909 | ||
MS01037 | 3EZE_B | 85 | -0.109 | 0.000 | 0.336 | 0.727 | NA | NA | 0.408 | 0.750 | 0.198 | 0.550 | ||
MS01038 | 3EZE_B | 85 | 0.288 | 0.543 | 0.364 | 0.704 | —— | —— | 0.375 | 0.731 | 0.086 | 0.429 | ||
MS01061* | 1MQ8_B | 177 | -0.051 | 0.000 | -0.020 | 0.000 | -0.041 | 0.000 | 0.009 | 0.081 | -0.030 | 0.000 | ||
MS01062 | 1MQ8_B | 177 | -0.030 | 0.000 | -0.062 | 0.000 | —— | —— | 0.024 | 0.135 | -0.041 | 0.000 | ||
MS01063 | 1MQ8_B | 177 | -0.027 | 0.000 | -0.039 | 0.000 | —— | —— | -0.018 | 0.065 | -0.031 | 0.000 | ||
MS01105/10/15* | 1II4_A | 155 | 0.059 | 0.385 | 0.163 | 0.545 | 0.095 | 0.571 | 0.233 | 0.523 | 0.274 | 0.750 | ||
MS01154* | 1HX1_A | 400 | -0.006 | 0.000 | 0.010 | 0.111 | -0.004 | 0.000 | 0.040 | 0.156 | 0.029 | 0.154 | ||
MS01190* | 1G1S_D | 28 | 0.386 | 0.750 | 0.388 | 0.636 | —— | —— | NA | NA | NA | NA | ||
MS01191 | 1G1S_D | 28 | 0.386 | 0.750 | 0.274 | 0.556 | —— | —— | NA | NA | NA | NA | ||
MS01192 | 1G1S_D | 28 | NA | NA | NA | NA | —— | —— | NA | NA | NA | NA |
2.2.3. Evaluation through sensitivity/1-specificity
MimoID | Antigen | EPI | Mapitope | PepSurf | Pepitope | Pep-3D-Search | EpiSearch | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sen | Spe | Sen | Spe | Sen | Spe | Sen | Spe | Sen | Spe | |||
Antigen-Antibody | ||||||||||||
MS00012* | 2OSL_P | 4 | NA | NA | 1.000 | 0.429 | NA | NA | 1.000 | 0.238 | 1.000 | 0.400 |
MS00013* | 3IU3_I | 28 | 0.286 | 0.979 | 0.214 | 0.897 | 0.107 | 0.985 | 0.571 | 0.908 | 0.357 | 0.949 |
MS00029* | 1TET_P | 11 | 0.636 | 1.000 | 0.727 | 1.000 | 0.636 | 1.000 | 0.818 | 0.750 | 1.000 | 1.000 |
MS00030 | 1TET_P | 11 | 0.455 | 1.000 | 0.818 | 1.000 | 0.455 | 1.000 | NA | NA | NA | NA |
MS00048* | 1YY9_A | 15 | 0.000 | 0.952 | 0.000 | 0.982 | 0.000 | 0.984 | 0.267 | 0.990 | 0.000 | 0.959 |
MS00049* | 1N8Z_C | 20 | 0.450 | 0.993 | 0.250 | 0.990 | 0.050 | 1.000 | 0.800 | 0.973 | 0.660 | 0.978 |
MS00052 | 2ADF_A | 15 | 0.200 | 0.978 | 0.667 | 0.956 | —— | —— | 0.933 | 0.862 | NA | NA |
MS00053* | 2ADF_A | 15 | 0.000 | 0.967 | 0.200 | 0.917 | 0.000 | 0.983 | 0.533 | 0.994 | 0.333 | 0.972 |
MS00054* | 1IQD_C | 16 | 0.938 | 0.350 | 0.125 | 0.857 | 0.125 | 1.000 | 0.375 | 0.714 | 0.562 | 0.886 |
MS00055* | 2GHW_A | 29 | 0.276 | 0.931 | 0.172 | 0.891 | —— | —— | 0.000 | 0.810 | 0.276 | 0.902 |
MS00056 | 2GHW_A | 29 | 0.276 | 0.943 | 0.345 | 0.908 | —— | —— | 0.000 | 0.787 | —— | —— |
MS00057 | 2NY7_G | 26 | 0.038 | 0.969 | 0.077 | 0.976 | —— | —— | 0.115 | 0.904 | 0.231 | 0.952 |
MS00058 | 2NY7_G | 26 | 0.000 | 0.973 | —— | —— | —— | —— | 0.077 | 0.924 | —— | —— |
MS00059* | 2NY7_G | 26 | 0.538 | 0.962 | 0.308 | 0.893 | 0.192 | 0.986 | 0.115 | 0.890 | 0.346 | 0.938 |
MS00099 | 1N8Z_C | 20 | 0.300 | 0.993 | 0.000 | 0.969 | NA | NA | 0.000 | 0.981 | 0.050 | 0.973 |
MS00185* | 1G9M_G | 15 | 0.733 | 0.924 | 0.467 | 0.922 | 0.467 | 0.967 | 0.133 | 0.859 | 0.000 | 0.922 |
MS00186* | 1E6J_P | 11 | 0.091 | 0.975 | 1.000 | 0.940 | 0.091 | 0.990 | 1.000 | 0.854 | 0.727 | 0.930 |
MS00242 | 2OSL_P | 4 | NA | NA | 1.000 | 0.238 | NA | NA | 1.000 | 0.238 | NA | NA |
Protein-Protein | ||||||||||||
MS00041* | 1OC0_B | 13 | 0.923 | 0.447 | 0.692 | 0.605 | 0.692 | 0.605 | 0.692 | 0.474 | 0.846 | 0.632 |
MS00047* | 1HX1_B | 22 | 0.227 | 0.826 | 0.409 | 0.826 | —— | —— | 0.227 | 0.728 | 0.545 | 0.859 |
MS00060* | 1WLP_B | 29 | 0.000 | 0.917 | 0.138 | 0.807 | 0.000 | 0.972 | 0.414 | 0.716 | —— | —— |
MS00062* | 1WLP_A | 16 | 0.938 | 0.556 | 0.625 | 0.556 | 0.500 | 1.000 | NA | NA | 0.562 | 1.000 |
MS00139* | 1K4U_S | 24 | 0.292 | 0.947 | 0.125 | 1.000 | 0.292 | 0.947 | 0.917 | 0.632 | —— | —— |
MS00276 | 2GRX_A | 36 | 0.000 | 0.980 | 0.167 | 0.975 | 0.000 | 0.987 | 0.028 | 0.946 | 0.056 | 0.961 |
MS00277* | 2GRX_A | 36 | 0.000 | 0.981 | 0.083 | 0.994 | 0.000 | 0.987 | 0.083 | 0.943 | 0.111 | 0.980 |
MS00278 | 2GSK_A | 42 | 0.000 | 0.989 | 0.143 | 0.991 | 0.000 | 0.998 | 0.119 | 0.974 | 0.000 | 0.947 |
MS00279* | 2GSK_A | 42 | 0.167 | 0.943 | 0.095 | 0.989 | 0.095 | 0.989 | 0.000 | 0.980 | 0.000 | 0.958 |
MS00357* | 1FLT_X | 21 | 0.381 | 0.959 | 0.143 | 0.986 | 0.143 | 0.986 | 0.238 | 0.770 | 0.524 | 0.932 |
MS00384* | 3DOW_B | 7 | 0.571 | 1.000 | 1.000 | 1.000 | 0.571 | 1.000 | NA | NA | NA | NA |
MS00405* | 1SHY_A | 27 | 0.087 | 0.934 | 0.174 | 0.924 | 0.043 | 0.981 | 0.130 | 0.853 | 0.043 | 0.900 |
MS00464 | 1SQ0_A | 27 | 0.148 | 0.973 | 0.111 | 0.930 | NA | NA | 0.259 | 0.845 | 0.259 | 0.925 |
MS00465* | 1SQ0_A | 27 | 0.000 | 0.957 | 0.074 | 0.930 | 0.000 | 0.968 | 0.222 | 0.893 | 0.185 | 0.952 |
MS00671* | 1D4V_B | 19 | 0.000 | 0.889 | 0.421 | 0.910 | 0.000 | 0.972 | 0.000 | 0.917 | 0.105 | 0.847 |
MS00976* | 3BT1_A | 27 | 0.407 | 0.972 | 0.148 | 0.713 | —— | —— | 0.593 | 0.898 | 0.222 | 0.824 |
MS00984* | 1EER_A | 38 | 0.132 | 0.953 | 0.053 | 0.953 | 0.000 | 0.984 | 0.132 | 0.961 | 0.079 | 0.922 |
MS01004 | 1MQ8_B | 17 | 0.000 | 0.919 | 0.000 | 0.925 | NA | NA | 0.118 | 0.831 | NA | NA |
MS01036* | 3EZE_B | 25 | 0.240 | 0.850 | 0.440 | 0.983 | 0.240 | 0.983 | 0.680 | 0.950 | 0.400 | 0.983 |
MS01037 | 3EZE_B | 25 | 0.000 | 0.917 | 0.640 | 0.900 | NA | NA | 0.840 | 0.883 | 0.440 | 0.850 |
MS01038 | 3EZE_B | 25 | 0.760 | 0.733 | 0.760 | 0.867 | —— | —— | 0.760 | 0.883 | 0.240 | 0.867 |
MS01061* | 1MQ8_B | 17 | 0.000 | 0.825 | 0.000 | 0.963 | 0.000 | 0.875 | 0.176 | 0.787 | 0.000 | 0.925 |
MS01062 | 1MQ8_B | 17 | 0.000 | 0.925 | 0.000 | 0.769 | —— | —— | 0.294 | 0.800 | 0.000 | 0.875 |
MS01063 | 1MQ8_B | 17 | 0.000 | 0.938 | 0.000 | 0.881 | —— | —— | 0.118 | 0.819 | 0.000 | 0.919 |
MS01105/10/15* | 1II4_A | 37 | 0.135 | 0.932 | 0.324 | 0.915 | 0.108 | 0.975 | 0.622 | 0.822 | 0.486 | 0.949 |
MS01154* | 1HX1_A | 21 | 0.000 | 0.989 | 0.048 | 0.979 | 0.000 | 0.995 | 0.333 | 0.900 | 0.190 | 0.942 |
MS01190* | 1G1S_D | 7 | 0.857 | 0.905 | 1.000 | 0.810 | —— | —— | NA | NA | NA | NA |
MS01191 | 1G1S_D | 7 | 0.857 | 0.905 | 0.714 | 0.810 | —— | —— | NA | NA | NA | NA |
MS01192 | 1G1S_D | 7 | NA | NA | NA | NA | —— | —— | NA | NA | NA | NA |
2.2.4. Overall performance evaluation
Statistics | Mapitope | PepSurf | Pepitope | Pep-3D-Search | EpiSearch |
---|---|---|---|---|---|
Antigen-Antibody | |||||
sensitivity | 0.326 | 0.434 | 0.212 | 0.455 | 0.426 |
specificity | 0.931 | 0.869 | 0.990 | 0.804 | 0.905 |
PPV | 0.407 | 0.334 | 0.580 | 0.273 | 0.345 |
MCC | 0.120 | 0.134 | 0.143 | 0.085 | 0.141 |
Protein-Protein | |||||
sensitivity | 0.254 | 0.305 | 0.149 | 0.333 | 0.241 |
specificity | 0.895 | 0.889 | 0.956 | 0.842 | 0.907 |
PPV | 0.311 | 0.409 | 0.330 | 0.288 | 0.317 |
MCC | 0.105 | 0.127 | 0.099 | 0.099 | 0.099 |
Benchmark dataset (Representative dataset) | |||||
sensitivity | 0.280(0.320) | 0.339(0.326) | 0.172(0.174) | 0.368(0.387) | 0.289(0.342) |
specificity | 0.908(0.890) | 0.892(0.901) | 0.968(0.965) | 0.841(0.845) | 0.921(0.922) |
PPV | 0.346(0.377) | 0.384(0.398) | 0.419(0.429) | 0.284(0.322) | 0.329(0.378) |
MCC | 0.112(0.127) | 0.129(0.126) | 0.116(0.112) | 0.092(0.101) | 0.112(0.139) |
3. Materials and Methods
3.1. Construction of the Datasets
Mimo_ID | PDB_ID | Template | Target | Library(1) | Ref (2) |
---|---|---|---|---|---|
Antigen-Antibody | |||||
MS00012* | 2OSL | B-lymphocyte antigen CD20 | Anti-CD20 monoclonal antibody rituximab | 13 × 9 | 16705086 |
MS00013* | 3IU3 | Interleukin-2 receptor subunit alpha | Anti-CD25 monoclonal antibody basiliximab | 6 × 9 | 17440057 |
MS00029* | 1TET | Heat-labile enterotoxin B chain | Anti-LTP-B monoclonal antibody TE33 | 10 × 9 | 16273596 |
MS00030 | 1TET | Heat-labile enterotoxin B chain | Anti-LTP-B monoclonal antibody TE33 | 5 × 11 | 16273596 |
MS00048* | 1YY9 | Epidermal growth factor receptor | Cetuximab | 4 × 12 | 16288119 |
MS00049* | 1N8Z | Receptor tyrosine-protein kinase erbB-2 | Trastuzumab | 5 × 12 | 15210798 |
MS00052 | 2ADF | von Willebrand factor | Anti-vWF monoclonal antibody 82D6A3 | 2 × 15 | 12855771 |
MS00053* | 2ADF | von Willebrand factor | Anti-vWF monoclonal antibody 82D6A3 | 3 × 8 | 12855771 |
MS00054* | 1IQD | Coagulation factor VIII | Anti-coagulation factor VIII monoclonal antibody BO2C11 | 27 × 12 | 12676786 |
MS00055* | 2GHW | Spike glycoprotein | Anti-spike glycoprotein monoclonal antibody 80R | 18 × 15 | 16630634 |
MS00056 | 2GHW | Spike glycoprotein | Anti-spike glycoprotein monoclonal antibody 80R | 9 × 16, 9 × 15, 19 × 14, 4 × 13 | 16630634 |
MS00057 | 2NY7 | Surface protein gp120 | Anti-gp120 monoclonal antibody b12 | 1 × 12, 1 × 15 | 16940148 |
MS00058 | 2NY7 | Surface protein gp120 | Anti-gp120 monoclonal antibody b12 | 1 × 6, 1 × 12, 1 × 13, 1 × 16, 1 × 18, 2 × 14, 2 × 20, 2 × 22 8 × 15, 13 × 21 | 16940148 |
MS00059* | 2NY7 | Surface protein gp120 | Anti-gp120 monoclonal antibody b12 | 1 × 10, 1 × 13, 17 × 14 | 16940148 |
MS00099 | 1N8Z | Receptor tyrosine-protein kinase erbB-2 | Trastuzumab | 2 × 12 | 15536075 |
MS00185* | 1G9M | Envelope glycoprotein gp120 | Anti-gp120 monoclonal antibody 17b | 10 × 12, 1 × 10 | 14596802 |
MS00186* | 1E6J | Capsid protein p24 | Anti-p42 monoclonal antibody 13b5 | 14 × 14, 2 × 7 | 14596802 |
MS00242 | 2OSL | B-lymphocyte antigen CD20 | Anti-CD20 monoclonal antibody rituximab | 7 × 12 | 16814270 |
Protein-Protein | |||||
MS00041* | 1OC0 | Vitronectin | Plasminogen activator inhibitor 1 | 8 × 13, 1 × 7, 1 × 11 | 16813566 |
MS00047* | 1HX1 | BAG family molecular chaperone regulator 1 | Heat shock cognate 71 kDa protein | 8 × 15 | 7649995 |
MS00060* | 1WLP | Neutrophil cytosol factor 1 | Cytochrome b-245 | 2 × 8, 31 × 9 | 7592831 |
MS00062* | 1WLP | Cytochrome b-245 light chain | Neutrophil cytosol factor 1 | 4 × 5, 3 × 9, 1 × 10, 1 × 8 | 7624379 |
MS00139* | 1K4U | Neutrophil cytosol factor 1 | Neutrophil cytosol factor 2 | 28 × 9, 2 × 10, 4 × 12, 2 × 6, 1 × 8 | 8663333 |
MS00276 | 2GRX | Ferrichrome-iron receptor | Protein tonB | 12 × 12 | 16414071 |
MS00277* | 2GRX | Ferrichrome-iron receptor | Protein tonB | 6 × 9 | 16414071 |
MS00278 | 2GSK | Vitamin B12 transporter btuB | Protein tonB | 2 × 12 | 16414071 |
MS00279* | 2GSK | Vitamin B12 transporter btuB | Protein tonB | 6 × 9 | 16414071 |
MS00357* | 1FLT | Vascular endothelial growth factor receptor 1 | Vascular endothelial growth factor A | 4 × 7 | 17401149 |
MS00384* | 3DOW | Calreticulin | Gamma-aminobutyric acid receptor-associated protein | 5 × 12 | 17916189 |
MS00405* | 1SHY | Hepatocyte growth factor | Hepatocyte growth factor receptor | 2 × 12, 1 × 13 | 17947467 |
MS00464 | 1SQ0 | von Willebrand factor | Platelet glycoprotein Ib alpha chain | 2 × 11 | 18363340 |
MS00465* | 1SQ0 | von Willebrand factor | Platelet glycoprotein Ib alpha chain | 3 ×11 | 18363340 |
MS00671* | 1D4V | Tumor necrosis factor ligand superfamily member 10 | Tumor necrosis factor receptor superfamily member 10B | 13 × 9 | 20156289 |
MS00976* | 3BT1 | Urokinase-type plasminogen activator | Urokinase plasminogen activator surface receptor | 19 × 15 | 8041758 |
MS00984* | 1EER | Erythropoietin | Erythropoietin receptor | 1 × 10 | 8662529 |
MS01004 | 1MQ8 | Integrin alpha-L beta-2 | Intercellular adhesion molecule 1 | 1 × 14 | 8953648 |
MS01036* | 3EZE | Phosphocarrier protein HPr | Phosphoenolpyruvate-protein phosphotransferase | 11 × 6 | 9350871 |
MS01037 | 3EZE | Phosphocarrier protein HPr | Phosphoenolpyruvate-protein phosphotransferase | 9 × 10 | 9350871 |
MS01038 | 3EZE | Phosphocarrier protein HPr | Phosphoenolpyruvate-protein phosphotransferase | 6 × 15 | 9350871 |
MS01061* | 1MQ8 | Integrin alpha-L beta-2 | Intercellular adhesion molecule 1 | 12 × 9, 1 × 8 | 11532073 |
MS01062 | 1MQ8 | Integrin alpha-L beta-2 | Intercellular adhesion molecule 1 | 1 × 9, 7 × 16 | 12963036 |
MS01063 | 1MQ8 | Integrin alpha-L beta-2 | Intercellular adhesion molecule 1 | 1 × 16 | 12963036 |
MS01105/10/15*(3) | 1II4 | Heparin-binding growth factor 2 | Fibroblast growth factor receptor 2 | 30 × 7 | 12032665 |
MS01154* | 1HX1 | Heat shock cognate 71 kDa protein | BAG family molecular chaperone regulator 1 | 8 × 12 | 11121403 |
MS01190* | 1G1S | P-selectin glycoprotein ligand 1 | P-selectin | 5 × 17 | 12393589 |
MS01191 | 1G1S | P-selectin glycoprotein ligand 1 | P-selectin | 2 × 15 | 12393589 |
MS01192 | 1G1S | P-selectin glycoprotein ligand 1 | P-selectin | 1 × 13, 1 × 18 | 12393589 |
3.2. Algorithm Evaluation
4. Conclusions
Authors’ Contribution
Additional Materials
Supplementary File 1
Supplementary File 2
Acknowledgements
References and Notes
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Sun, P.; Chen, W.; Huang, Y.; Wang, H.; Ma, Z.; Lv, Y. Epitope Prediction Based on Random Peptide Library Screening: Benchmark Dataset and Prediction Tools Evaluation. Molecules 2011, 16, 4971-4993. https://doi.org/10.3390/molecules16064971
Sun P, Chen W, Huang Y, Wang H, Ma Z, Lv Y. Epitope Prediction Based on Random Peptide Library Screening: Benchmark Dataset and Prediction Tools Evaluation. Molecules. 2011; 16(6):4971-4993. https://doi.org/10.3390/molecules16064971
Chicago/Turabian StyleSun, Pingping, Wenhan Chen, Yanxin Huang, Hongyan Wang, Zhiqiang Ma, and Yinghua Lv. 2011. "Epitope Prediction Based on Random Peptide Library Screening: Benchmark Dataset and Prediction Tools Evaluation" Molecules 16, no. 6: 4971-4993. https://doi.org/10.3390/molecules16064971