Teyra Joan, Doms Andreas, Schroeder Michael, Pisabarro M Teresa
Department of Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany.
BMC Bioinformatics. 2006 Mar 2;7:104. doi: 10.1186/1471-2105-7-104.
Currently there is a strong need for methods that help to obtain an accurate description of protein interfaces in order to be able to understand the principles that govern molecular recognition and protein function. Many of the recent efforts to computationally identify and characterize protein networks extract protein interaction information at atomic resolution from the PDB. However, they pay none or little attention to small protein ligands and solvent. They are key components and mediators of protein interactions and fundamental for a complete description of protein interfaces. Interactome profiling requires the development of computational tools to extract and analyze protein-protein, protein-ligand and detailed solvent interaction information from the PDB in an automatic and comparative fashion. Adding this information to the existing one on protein-protein interactions will allow us to better understand protein interaction networks and protein function.
SCOWLP (Structural Characterization Of Water, Ligands and Proteins) is a user-friendly and publicly accessible web-based relational database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database includes proteins, peptidic-ligands and interface water molecules as descriptors of protein interfaces. It contains currently 74,907 protein interfaces and 2,093,976 residue-residue interactions formed by 60,664 structural units (protein domains and peptidic-ligands) and their interacting solvent. The SCOWLP web-server allows detailed structural analysis and comparisons of protein interfaces at atomic level by text query of PDB codes and/or by navigating a SCOP-based tree. It includes a visualization tool to interactively display the interfaces and label interacting residues and interface solvent by atomic physicochemical properties. SCOWLP is automatically updated with every SCOP release.
SCOWLP enriches substantially the description of protein interfaces by adding detailed interface information of peptidic-ligands and solvent to the existing protein-protein interaction databases. SCOWLP may be of interest to many structural bioinformaticians. It provides a platform for automatic global mapping of protein interfaces at atomic level, representing a useful tool for classification of protein interfaces, protein binding comparative studies, reconstruction of protein complexes and understanding protein networks. The web-server with the database and its additional summary tables used for our analysis are available at http://www.scowlp.org.
目前迫切需要有助于准确描述蛋白质界面的方法，以便能够理解支配分子识别和蛋白质功能的原理。最近许多通过计算识别和表征蛋白质网络的努力，都是从蛋白质数据银行（PDB）中以原子分辨率提取蛋白质相互作用信息。然而，它们对小蛋白质配体和溶剂关注甚少或根本没有关注。它们是蛋白质相互作用的关键组成部分和媒介，对于完整描述蛋白质界面至关重要。相互作用组分析需要开发计算工具，以便以自动和比较的方式从PDB中提取和分析蛋白质-蛋白质、蛋白质-配体以及详细的溶剂相互作用信息。将这些信息添加到现有的蛋白质-蛋白质相互作用信息中，将使我们能够更好地理解蛋白质相互作用网络和蛋白质功能。
SCOWLP（水、配体和蛋白质的结构表征）是一个基于网络的用户友好型公共关系数据库，用于对PDB蛋白质界面进行详细表征和可视化。SCOWLP数据库包括蛋白质、肽配体和界面水分子作为蛋白质界面的描述符。它目前包含由60,664个结构单元（蛋白质结构域和肽配体）及其相互作用的溶剂形成的74,907个蛋白质界面和2,093,976个残基-残基相互作用。SCOWLP网络服务器允许通过PDB代码的文本查询和/或通过浏览基于结构分类（SCOP）的树，在原子水平上对蛋白质界面进行详细的结构分析和比较。它包括一个可视化工具，以交互方式显示界面，并根据原子物理化学性质标记相互作用的残基和界面溶剂。SCOWLP会随着每次SCOP版本自动更新。
SCOWLP通过将肽配体和溶剂的详细界面信息添加到现有的蛋白质-蛋白质相互作用数据库中，极大地丰富了对蛋白质界面的描述。SCOWLP可能会引起许多结构生物信息学家的兴趣。它提供了一个在原子水平上自动全局映射蛋白质界面的平台，是蛋白质界面分类、蛋白质结合比较研究、蛋白质复合物重建以及理解蛋白质网络的有用工具。带有数据库及其用于我们分析的附加汇总表的网络服务器可在http://www.scowlp.org上获取。
