College of Chemistry, Sichuan University, Chengdu, 610064, PR China.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W385-90. doi: 10.1093/nar/gkr284. Epub 2011 May 23.
Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein-protein and protein-small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein-protein and protein-small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein-protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.
序列衍生的结构和物理化学特性已被广泛用于分析和预测蛋白质和肽的结构、功能、表达和相互作用谱。PROFEAT 已被开发为一个网络服务器，用于根据氨基酸序列计算蛋白质和肽的常用特性。为了促进对蛋白质和肽的更广泛研究，PROFEAT 进行了许多改进和更新。我们添加了新的功能，用于计算蛋白质-蛋白质和蛋白质-小分子相互作用的描述符、蛋白质序列局部特性的片段描述符、肽序列和小分子结构的拓扑描述符。我们还为蛋白质和肽添加了新的特征组（伪氨基酸组成、两亲性伪氨基酸组成、总氨基酸特性和原子水平拓扑描述符）以及小分子（原子水平拓扑描述符）。总的来说，PROFEAT 为蛋白质和肽计算了 11 个特征组的描述符，为小分子计算了一个包含 400 多个描述符的特征组，以及蛋白质-蛋白质和蛋白质-小分子相互作用的衍生特征。我们的计算算法已经在许多已发表的工作中进行了广泛的测试和应用，用于预测特定结构或功能类别的蛋白质、蛋白质-蛋白质相互作用、特定功能的肽以及小分子的定量结构活性关系。PROFEAT 可在 http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi 免费获得。
