翻译后修饰(PTMs)是指一些蛋白质在生物合成后的氨基酸侧链修饰。有超过400种不同类型的PTMs影响着蛋白质功能的许多方面。这种修饰作为关键的分子调节机制发生,以调节各种细胞过程。这些过程对蛋白质的结构和功能有重大影响。PTMs的破坏会导致重要生物过程的功能障碍,从而导致各种疾病。发现PTMs的高通量实验方法是非常费力和耗时的。因此,迫切需要计算方法和强大的工具来预测PTMs。目前有大量的PTMs数据,这些数据可以通过许多在线数据库公开获取。
PTM示意性的流程图,显示了预测器如何为PTM预测工作。(A) 数据收集和数据集创建。(B) 特征选择。(C) 创建训练和测试模型。(D) 评价模型的性能。
General statistics | ||||||
---|---|---|---|---|---|---|
简称Acronym | 覆盖的物种数量 | PTM类型数量 | Number of PTMsa | 数据和数据库的类型b | URL网站 | |
General database | dbPTM | More than 1000 organisms | 130 | S: ∼908 900 P: ∼557 700 |
Exp. and Pred. Secondary |
http://dbptm.mbc.nctu.edu.tw |
BioGRID | 71 organisms | 6 | S: ∼700 000 P: ∼419 400 |
Exp. Primary |
https://orcs.thebiogrid.org | |
Phosphosite Plus | 26 organisms | 7 | S: ∼483 700 P: ∼20 200 |
Exp. Primary |
https://www.phosphosite.org | |
PTMCode v2 | 19 organisms | 69 | S: ∼316 500 P: ∼ 45 300 |
Exp. Secondary |
http://ptmcode.embl.de | |
qPTM | Human | 10 | S: ∼296 900 P: ∼19 600 |
Exp. Secondary |
http://qptm.omicsbio.info/ | |
PLMD | 176 organisms | 20 | S: ∼285 700 P: ∼53 500 |
Exp. Secondary |
http://plmd.biocuckoo.org | |
CPLM | 122 organisms | 12 | S: ∼189 900 P: ∼45 700 |
Exp. Secondary |
http://cplm.biocuckoo.org | |
YAAM | Saccharomyces cerevisiae | 19 | S: ∼121 900 P: ∼680 |
Exp. Secondary |
http://yaam.ifc.unam.mx | |
HPRD | Human | 9 | S: ∼ 93 700 P: ∼30 000 |
Exp. Primary |
http://www.hprd.org | |
PHOSIDA | 9 organisms | 3 | S: ∼80 000 P: ∼28 700 |
Exp. Secondary |
http://www.phosida.com | |
PTM-SD | 7 model organisms | 21 | S: ∼10 600 P: ∼842 |
Exp. Secondary |
http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD | |
WERAM | 8 organisms | 2 | S: ∼ 900 P: ∼584 |
Exp. Secondary |
http://weram.biocuckoo.org | |
Phosphorylation
磷酸化 | EPSD | 68 organisms | Phosphorylation | S: ∼1 616 800 P: ∼209 300 | Exp. Secondary | http://epsd.biocuckoo.cn |
PhosphoNET | Human | Phosphorylation | S: ∼950 000 P: ∼20 000 | Exp. and Pred. Secondary | http://www.phosphonet.ca | |
RegPhos | Human, mouse and rat | Phosphorylation | S: ∼111 700 P: ∼ 18 700 | Exp. and Pred. Secondary | http://140.138.144.141/∼RegPhos | |
Phospho.ELM | Mainly model organisms | Phosphorylation | S: ∼42 900 P: ∼8600 | Exp. Secondary | http://phospho.elm.eu.org | |
Phospho3D | Mainly model organisms | Phosphorylation | S: ∼42 500 P: ∼8700 | Exp. Secondary | http://www.phospho3d.org | |
dbPSP | 200 prokaryotic organisms | Phosphorylation | S: ∼19 300 P: ∼8600 | Exp. Secondary | http://dbpsp.biocuckoo.cn/indExp.php | |
pTestis | Mouse | Phosphorylation | S: ∼17 800 P: ∼3900 | Exp. and Pred. Secondary | http://ptestis.biocuckoo.org | |
LymPHOS | Human | Phosphorylation | S: ∼15 500 P: ∼4900 | Exp. and Pred. Primary | https://www.lymphos.org | |
P3DB | 9 plant organisms | Phosphorylation | S: ∼14 600 P: ∼6400 | Exp. and Pred. | http://www.p3db.org | |
Glycosylation
糖基化 | UniPep | Human | N-glycosylation | S: ∼52 400 P: ∼40 100 | Exp. and Pred. | http://www.unipep.org |
GlycoFly | Drosophila melanogaster | N-glycosylation | S: ∼740 P: ∼477 | Exp. and Pred. | http://betenbaugh.jhu.edu/GlycoFly | |
GlycoFish | Zebrafish | N-glycosylation | S: ∼269 P: ∼169 | Exp. and Pred. Primary | http://betenbaugh.jhu.edu/GlycoFish | |
Ubiquitylation
泛素化 | mUbiSiDa | 7 model organisms | Ubiquitylation | S: ∼110 900 P: ∼ 35 400 | Exp. Secondary | http://reprod.njmu.edu.cn/mUbiSiDa |
S-palmitoylation
棕榈酰化 | SwissPalm | 17 organisms | S-palmitoylation | S: ∼1062 P: ∼664 | Exp. and Pred. Secondary | https://swisspalm.org |
S-nitrosylation
亚硝化作用 | dbSNO | 18 organisms | S-nitrosylation | S: ∼4200 P: ∼2200 | Exp. Secondary | http://dbSNO.mbc.nctu.edu.tw |
aa:PTM位点和修饰蛋白的数量,分别缩写为S和P
b:Type of data’可以是实验性的和/或预测性的,分别简写为Exp.和Pred.。
‘Type of database’可以是主要的或次要的。如果一个数据库是其他一些数据库的整合,则被认为是二级数据库。
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