Table 2.
Improvement of the performance of the AutoMotifServer 3.0.
| AMS 2.0 | AMS 3.0 | AMS 3.0 (New SwissProt dataset) | |||||||
|---|---|---|---|---|---|---|---|---|---|
| PTM type | Agent | Recall | Precision | Recall | Precision | AUC | Recall | Precision | AUC |
| 3,4-dihydroxyproline | - | 88,89 | 66,67 | 95,45 | 87,5 | 0,962273 | 97,37 | 97,37 | 0,985088 |
| 4-carboxyglutamate | - | 90,56 | 95,93 | 96,27 | 99,65 | 0,980856 | 96,54 | 99,35 | 0,982076 |
| 4-hydroxyproline | - | 65,59 | 85,31 | 86,88 | 83,94 | 0,905902 | 95,03 | 94,14 | 0,969559 |
| 5-hydroxylysine | - | 12,79 | 84,62 | 97,3 | 38,92 | 0,845236 | 90,16 | 95,93 | 0,948272 |
| Asymmetric dimethylarginine | - | 84,62 | 82,09 | 94,55 | 94,55 | 0,965227 | - | - | - |
| dihydroxyphenylalanine | - | 29,41 | 76,92 | 86,17 | 86,17 | 0,914601 | - | - | - |
| Glycine amide | - | 84,38 | 90 | 97,92 | 97,92 | 0,977679 | 99,3 | 99,3 | 0,984574 |
| Hydroxyproline | - | 28,8 | 85,71 | 89,62 | 94,06 | 0,942113 | 94,62 | 99,19 | 0,972567 |
| Leucine amide | - | 98,97 | 97,96 | 98,1 | 99,36 | 0,989049 | - | - | - |
| Methionine amide | - | 100 | 93,75 | 100 | 93,75 | 0,666667 | - | - | - |
| N-acetylglycine | - | 79,17 | 90,48 | 97,83 | 97,83 | 0,985797 | - | - | - |
| N-acetylmethionine | - | 100 | 95,42 | 98,4 | 98,93 | 0,990593 | - | - | - |
| N-acetylserine | - | 98,24 | 99,64 | 98,22 | 99,4 | 0,990124 | - | - | - |
| N-acetylthreonine | - | 76,47 | 88,64 | 89,8 | 97,78 | 0,94648 | - | - | - |
| N6-acetyllysine | - | 12,76 | 74,32 | 94,3 | 93,23 | 0,953465 | - | - | - |
| N6, N6, N6-trimethyllysine | - | 7,5 | 60 | 85,71 | 97,5 | 0,926065 | - | - | - |
| Omega-N-methylated arginine | - | 0 | 0 | 78 | 58,21 | 0,82 | - | - | - |
| Phenylalanine amide | - | 98,59 | 93,33 | 99 | 99 | 0,986667 | - | - | - |
| Phospho | PKA | 63,64 | 77,78 | 90,72 | 86,27 | 0,939608 | 97,39 | 95,39 | 0,983802 |
| Phospho | PKC | 32,56 | 84,85 | 86,17 | 97,59 | 0,928851 | 94,78 | 99,18 | 0,973369 |
| Phospho | autocatalysis | 13,16 | 96,15 | 79,35 | 93,59 | 0,888392 | 95,96 | 99,15 | 0,97851 |
| Phospho | CDC2 | 85,71 | 80,9 | 89,55 | 75,95 | 0,916095 | 93,73 | 92,36 | 0,963488 |
| Phosphoserine | - | 97,06 | 91,34 | 94,33 | 95,56 | 0,94975 | 96,87 | 98,02 | 0,912848 |
| Phosphoserine | PKA | 68,42 | 78,31 | 91,67 | 72,64 | 0,922083 | 97,66 | 98,43 | 0,987096 |
| Phosphoserine | PKC | 23,29 | 80,95 | 96,43 | 95,29 | 0,975476 | 94,93 | 98,94 | 0,973939 |
| Phosphoserine | autocatalysis | 10 | 85,71 | 75 | 90,7 | 0,868311 | 91,57 | 99,13 | 0,957295 |
| Phosphoserine | CK2 | 29,73 | 70,97 | 88,14 | 59,77 | 0,882345 | 93,02 | 98,23 | 0,962999 |
| Phosphothreonine | - | 46,12 | 75,46 | 78,16 | 69,73 | 0,828495 | 85,2 | 97,4 | 0,905598 |
| Phosphothreonine | autocatalysis | 0 | 0 | 73,47 | 80 | 0,849347 | 94,96 | 99,82 | 0,974381 |
| Phosphotyrosine | - | 9,32 | 71,2 | 84,24 | 96,69 | 0,91775 | 91,75 | 98,97 | 0,952053 |
| Phosphotyrosine | autocatalysis | 1,41 | 12,5 | 92 | 92 | 0,951404 | 96,82 | 97,21 | 0,979045 |
| Pyrrolidone carboxylic acid | - | 60,31 | 97,11 | 91,58 | 97,92 | 0,955236 | - | - | - |
| Sulfotyrosine | - | 70,19 | 85,88 | 98,39 | 97,6 | 0,988929 | 99,48 | 98,47 | 0,990853 |
| Valine amide | - | 94,29 | 97,06 | 98,57 | 98,57 | 0,986607 | - | - | - |
| Phospho.ELM | - | 98 | 91,68 | - | - | - | 98,56 | 96,07 | 0,949397 |
| Phospho.ELM | Abl | 0 | 0 | - | - | - | 81,82 | 52,94 | 0,862032 |
| Phospho.ELM | AMPK_group | 6,25 | 100 | - | - | - | 100 | 72,22 | 0,975 |
| Phospho.ELM | ATM | 92,98 | 81,54 | - | - | - | 94,87 | 90,24 | 0,967439 |
| Phospho.ELM | CaM-KIIalpha | 41,67 | 88,24 | - | - | - | 100 | 77,42 | 0,981081 |
| Phospho.ELM | CaM-KII_group | 14,55 | 88,89 | - | - | - | 82,05 | 94,12 | 0,906796 |
| Phospho.ELM | CDK1 | 41,73 | 63,04 | - | - | - | 96,94 | 62,91 | 0,94711 |
| Phospho.ELM | CDK2 | 7,14 | 45,45 | - | - | - | 92,31 | 64,86 | 0,928627 |
| Phospho.ELM | CDK_group | 59,8 | 67,03 | - | - | - | 95,65 | 67,35 | 0,947785 |
| Phospho.ELM | CK1_group | 0 | 0 | - | - | - | 86,67 | 72,22 | 0,911594 |
| Phospho.ELM | CK2 alpha | 38,98 | 67,65 | - | - | - | 78,82 | 70,53 | 0,872036 |
| Phospho.ELM | CK2_group | 43,33 | 72,22 | - | - | - | 73,33 | 64,36 | 0,839759 |
| Phospho.ELM | EGFR | 0 | 0 | - | - | - | 73,17 | 78,95 | 0,852909 |
| Phospho.ELM | Fyn | 0 | 0 | - | - | - | 87,5 | 84,85 | 0,9275 |
| Phospho.ELM | GRK_group | 2,7 | 100 | - | - | - | 83,33 | 90,91 | 0,911404 |
| Phospho.ELM | GSK-3beta | 18,37 | 75 | - | - | - | 85,29 | 64,44 | 0,896282 |
| Phospho.ELM | GSK-3_group | 12,5 | 66,67 | - | - | - | 65,22 | 93,75 | 0,823128 |
| Phospho.ELM | IGF1R | 26,09 | 100 | - | - | - | 85 | 73,91 | 0,90625 |
| Phospho.ELM | IKK_group | 0 | 0 | - | - | - | 95,83 | 92 | 0,973761 |
| Phospho.ELM | InsR | 6,67 | 60 | - | - | - | 70,97 | 88 | 0,848289 |
| Phospho.ELM | Lck | 11,76 | 60 | - | - | - | 80,56 | 74,36 | 0,884596 |
| Phospho.ELM | Lyn | 0 | 0 | - | - | - | 66,67 | 84,62 | 0,825137 |
| Phospho.ELM | MAPK1 | 45,88 | 67,24 | - | - | - | 88,98 | 55,85 | 0,898547 |
| Phospho.ELM | MAPK14 | 4 | 22,22 | - | - | - | 82,35 | 77,78 | 0,896017 |
| Phospho.ELM | MAPK3 | 74,7 | 78,48 | - | - | - | 87,93 | 77,27 | 0,922801 |
| Phospho.ELM | MAPK8 | 14,71 | 41,67 | - | - | - | 91,67 | 84,62 | 0,947523 |
| Phospho.ELM | MAPKAPK2 | 3,03 | 100 | - | - | - | 69,57 | 80 | 0,836332 |
| Phospho.ELM | MAPK_group | 54,9 | 77,78 | - | - | - | 82,35 | 75,68 | 0,894784 |
| Phospho.ELM | PDK-1 | 42,86 | 85,71 | - | - | - | 80 | 95,24 | 0,897283 |
| Phospho.ELM | PKA alpha | 42,42 | 82,35 | - | - | - | 86,96 | 95,24 | 0,931824 |
| Phospho.ELM | PKA_group | 58,15 | 90,43 | - | - | - | 91,74 | 62,99 | 0,904783 |
| Phospho.ELM | PKB_group | 79,76 | 65,05 | - | - | - | 88,14 | 77,61 | 0,924011 |
| Phospho.ELM | PKC alpha | 19,7 | 72,22 | - | - | - | 75,56 | 48,57 | 0,825223 |
| Phospho.ELM | PKC_group | 25,21 | 80 | - | - | - | 82,02 | 84,39 | 0,900038 |
| Phospho.ELM | PLK1 | 0 | 0 | - | - | - | 68,97 | 45,45 | 0,788753 |
| Phospho.ELM | Src | 0,67 | 5 | - | - | - | 74,31 | 65,32 | 0,845308 |
| Phospho.ELM | Syk | 6,67 | 30 | - | - | - | 85,71 | 53,57 | 0,878378 |
Comparison of best performances of the AMS 2.0 server with the current AMS version 3.0 on best results obtained on the training datasets of respective PTM types.