Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
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DOI：
10.1093/nar/gkg584
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Yaffe, MB
中科院分区：
文献类型：
--
作者：
Obenauer, JC;Cantley, LC;Yaffe, MB
Scansite识别由模块化信号结构域识别、由蛋白质Ser/Thr-或Tyr-激酶磷酸化或介导与蛋白质或磷脂配体的特异性相互作用的短蛋白质序列基序。基于定向肽库和噬菌体展示实验的结果，每个序列基序被表示为位置特异性评分矩阵（PSSM）。从Scansite预测的结构域基序相互作用可以顺序组合，允许生物途径的片段在计算机上构建。Scansite 2.0版的当前版本包括62个基序，这些基序表征了许多Ser/Thr-或Tyr-激酶家族、SH 2、SH 3、PDZ、14-3-3和PTB结构域的结合和/或底物特异性，以及PtdIns（3，4，5）P-3特异性PH结构域的特征基序。Scansite 2.0包含对其原始界面的重大改进，包括许多新的通用用户功能和显著增强的性能。所有SWISS-PROT、TrEMBL、Genpept和Ensembl蛋白质数据库条目的扫描现在都可以实现，与Scansite 1.0版相比，运行时间减少了60%。Scansite 2.0允许物种特异性蛋白质的有限搜索，以及等电点和分子量分选，以便于预测结果与二维凝胶电泳实验的比较。增加了对用户自定义基序的支持，允许更容易地输入用户自定义矩阵，并允许用户自定义基序与预编译的Scansite基序相结合，以进行双基序搜索。此外，一个新的系列的序列匹配程序的非定量用户定义的图案已经实施。Scansite可通过万维网http://scansite.mit.edu获得。
Scansite identifies short protein sequence motifs that are recognized by modular signaling domains, phosphorylated by protein Ser/Thr- or Tyr-kinases or mediate specific interactions with protein or phospholipid ligands. Each sequence motif is represented as a position-specific scoring matrix (PSSM) based on results from oriented peptide library and phage display experiments. Predicted domain-motif interactions from Scansite can be sequentially combined, allowing segments of biological pathways to be constructed in silico. The current release of Scansite, version 2.0, includes 62 motifs characterizing the binding and/or substrate specificities of many families of Ser/Thr- or Tyr-kinases, SH2, SH3, PDZ, 14-3-3 and PTB domains, together with signature motifs for PtdIns(3,4,5)P-3-specific PH domains. Scansite 2.0 contains significant improvements to its original interface, including a number of new generalized user features and significantly enhanced performance. Searches of all SWISS-PROT, TrEMBL, Genpept and Ensembl protein database entries are now possible with run times reduced by similar to60% when compared with Scansite version 1.0. Scansite 2.0 allows restricted searching of species-specific proteins, as well as isoelectric point and molecular weight sorting to facilitate comparison of predictions with results from two-dimensional gel electrophoresis experiments. Support for user-defined motifs has been increased, allowing easier input of user-defined matrices and permitting user-defined motifs to be combined with pre-compiled Scansite motifs for dual motif searching. In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu.