Analysis and prediction of the critical regions of antimicrobial peptides based on conditional random fields.
Analysis and prediction of the critical regions of antimicrobial peptides based on conditional random fields.
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DOI：
10.1371/journal.pone.0119490
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Wang CK
中科院分区：
文献类型：
--
作者：
Chang KY;Lin TP;Shih LY;Wang CK
抗菌肽（AMPs）是抗细菌、真菌、寄生虫和病毒等微生物的有效候选药物。amp的大小从不足10个到数百个氨基酸不等。通常只有少数氨基酸或抗菌蛋白的关键区域与功能有关。准确预测AMP临界区域有助于实验设计。然而，目前还没有对AMP临界区域进行专门的广泛分析，对它们的计算建模要么是不存在的，要么是解决了其他问题。因此，我们通过引入最先进的机器学习方法——条件随机场，开发了一个AMP关键区域的计算模型。我们生成了798个AMP核心的综合数据集和510个代表性AMP核心的低相似性数据集。amcore在综合数据集上的最大准确率为90%，马修相关系数为0.79；在低相似度数据集上的最大准确率为83%，马修相关系数为0.66。我们对AMP核心的分析遵循我们对AMP的了解：甘氨酸和赖氨酸含量高，但天冬氨酸、谷氨酸和蛋氨酸含量低；α-螺旋结构的丰度；正电荷占主导地位；两亲性的特性。在AMP核内发现了两个两亲性序列基序，即α-两亲性螺旋和π-两亲性螺旋。此外，首次报道了AMP核核n端边界的短序列基序：AMP核核P（-1）处的精氨酸与P1处的甘氨酸偶联最多，这可能与微生物细胞粘附有关。
Antimicrobial peptides (AMPs) are potent drug candidates against microbes such as bacteria, fungi, parasites, and viruses. The size of AMPs ranges from less than ten to hundreds of amino acids. Often only a few amino acids or the critical regions of antimicrobial proteins matter the functionality. Accurately predicting the AMP critical regions could benefit the experimental designs. However, no extensive analyses have been done specifically on the AMP critical regions and computational modeling on them is either non-existent or settled to other problems. With a focus on the AMP critical regions, we thus develop a computational model AMPcore by introducing a state-of-the-art machine learning method, conditional random fields. We generate a comprehensive dataset of 798 AMPs cores and a low similarity dataset of 510 representative AMP cores. AMPcore could reach a maximal accuracy of 90% and 0.79 Matthew’s correlation coefficient on the comprehensive dataset and a maximal accuracy of 83% and 0.66 MCC on the low similarity dataset. Our analyses of AMP cores follow what we know about AMPs: High in glycine and lysine, but low in aspartic acid, glutamic acid, and methionine; the abundance of α-helical structures; the dominance of positive net charges; the peculiarity of amphipathicity. Two amphipathic sequence motifs within the AMP cores, an amphipathic α-helix and an amphipathic π-helix, are revealed. In addition, a short sequence motif at the N-terminal boundary of AMP cores is reported for the first time: arginine at the P(-1) coupling with glycine at the P1 of AMP cores occurs the most, which might link to microbial cell adhesion.
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影响因子：
2.9
作者：
Fernandes, Fabiano C.;Rigden, Daniel J.;Franco, Octavio L.
通讯作者：
Franco, Octavio L.
DOI：
10.1016/0305-0491(71)90258-6
发表时间：
1971-01-01
期刊：
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY
影响因子：
--
作者：
MASSON, PL;HEREMANS, JF
通讯作者：
HEREMANS, JF
影响因子：
2.7
作者：
LIU, DC;NOCEDAL, J
通讯作者：
NOCEDAL, J
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A