Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W53-8. doi: 10.1093/nar/gkq522. Epub 2010 Jun 10.
ProteinDBS v2.0 is a web server designed for efficient and accurate comparisons and searches of structurally similar proteins from a large-scale database. It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches of protein structures or substructures. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison. The experimental results show that our system is able to return results of global comparisons in seconds from a complete Protein Data Bank (PDB) database of 152,959 protein chains and that it takes much less time to complete local comparisons from a non-redundant database of 3276 proteins than other accurate comparison methods. ProteinDBS v2.0 supports query by PDB protein ID and by new structures uploaded by users. To our knowledge, this is the only search engine that can simultaneously support global and local comparisons. ProteinDBS v2.0 is a useful tool to investigate functional or evolutional relationships among proteins. Moreover, the common substructures identified by local comparison can be potentially used to assist the human curation process in discovering new domains or folds from the ever-growing protein structure databases. The system is hosted at http://ProteinDBS.rnet.missouri.edu.
ProteinDBS v2.0 是一个旨在实现高效、准确地比较和搜索大规模数据库中结构相似蛋白质的网络服务器。它提供了全局到全局和局部到局部两种比较方法，以方便蛋白质结构或子结构的搜索。ProteinDBS v2.0 应用了先进的特征提取算法和可扩展的索引技术，在保持相当高的结构比较精度的同时，实现了高速运行。实验结果表明，我们的系统能够在几秒钟内从包含 152959 条蛋白质链的完整蛋白质数据库（PDB）中返回全局比较的结果，并且与其他准确的比较方法相比，从非冗余数据库（包含 3276 条蛋白质）中进行局部比较所需的时间要少得多。ProteinDBS v2.0 支持通过 PDB 蛋白质 ID 和用户上传的新结构进行查询。据我们所知，这是唯一一个可以同时支持全局和局部比较的搜索引擎。ProteinDBS v2.0 是研究蛋白质之间功能或进化关系的有用工具。此外，通过局部比较识别的常见子结构可以潜在地用于协助人类从不断增长的蛋白质结构数据库中发现新的结构域或折叠的过程。该系统托管在 http://ProteinDBS.rnet.missouri.edu。
