Abstract
BackgroundThe molecular network sustained by different types of interactions among proteins is widely manifested as the fundamental driving force of cellular operations. Many biological functions are determined by the crosstalk between proteins rather than by the characteristics of their individual components. Thus, the searches for protein partners in global networks are imperative when attempting to address the principles of biology.ResultsWe have developed a web-based tool “Sequence-based Protein Partners Search” (SPPS) to explore interacting partners of proteins, by searching over a large repertoire of proteins across many species. SPPS provides a database containing more than 60,000 protein sequences with annotations and a protein-partner search engine in two modes (Single Query and Multiple Query). Two interacting proteins of human FBXO6 protein have been found using the service in the study. In addition, users can refine potential protein partner hits by using annotations and possible interactive network in the SPPS web server.ConclusionsSPPS provides a new type of tool to facilitate the identification of direct or indirect protein partners which may guide scientists on the investigation of new signaling pathways. The SPPS server is available to the public at http://mdl.shsmu.edu.cn/SPPS/.
Highlights
The molecular network maintained by different types of protein interactions is widely manifested as the fundamental driving force of cellular operations [1]
Outline of Sequence-based Protein Partners Search (SPPS) server The SPPS server consists of two parts, a front-end web interface written in Ajax framework ExtJS, with MySQL as the database system, and a back-end program ‘‘Kangaroo’’ for protein partners searching on a Linux Cluster server
SPPS server provides two modes, ‘‘Single Query’’ mode and ‘‘Multiple Query’’ mode, to capture interacting partners for query protein. ‘‘Single Query’’ mode applies one query protein sequence to fish out its potential partners in a species-specific database. ‘‘Multiple Query’’ mode makes a rapid estimation of direct and indirect interactions between two query protein sequences
Summary
The molecular network maintained by different types of protein interactions is widely manifested as the fundamental driving force of cellular operations [1]. Crosstalk between proteins instead of individual components leads to many biological functions [2]. Different means of discovering protein partners in the global network have been considerably valued since these are required to address the imperative principles of biological systems [3]. The molecular network sustained by different types of interactions among proteins is widely manifested as the fundamental driving force of cellular operations. Many biological functions are determined by the crosstalk between proteins rather than by the characteristics of their individual components. The searches for protein partners in global networks are imperative when attempting to address the principles of biology
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