SPPS : Sequence-based Protein Partner Search  
Introduction   Query One   Query Two   Result   Document   Forum

The molecular network sustained by different types of interactions among proteins is widely manifested as fundamental drive of cellular operations. Many biological functions are more closely determined by crosstalk between protein and its partners than by the characteristics of their individual component. Thus, protein partners search in global network have been unprecedentedly appreciated due to the requirement to address the general principles of biological systems by means of systems biology. However, protein partners search in the network using a large-scale yeast two-hybrid or coimmunprecipitation is time-consuming and costly due to the lack of suggestive knowledge and specific direction. Therefore, a universal tool, which can predict most possible protein partners in advance, is helpful to enhance the efficiency of protein partners search by experiments.

It is virtually axiomatic that “sequence specifies structure”, which gives rise to an assumption that knowledge of the amino acid sequence alone might be sufficient to estimate the interacting propensity between two proteins for a specific biological function. Accordingly, prediction of protein partners only based on sequence information is ideal approach combined rapidity with generality. Herein, we present a web-based tool Sequence-based Protein Partners Search (SPPS) for rapidly predicting potential partners for a given protein sequence.  To our knowledge, SPPS is the first web server for rapidly searching universal protein partners from amongst thousands of candidate proteins in multiple species. It makes use of a machine learning algorithm─support vector machine (SVM) to search out all possible protein partners for a query protein from a series of protein databases covering several species. Furthermore, SPPS enables analysis of possible protein partners derived from search in terms of some defined filters, such as subcellular location, tissue distribution, protein function, relative disease and so on. The query protein might be a key enzyme detected in biochemical or signaling transduction experiments, a regulatory factor in the network or a novel protein whose functions is unknown. Thus, SPPS may serve as a valuable tool for identifying protein partners in the network for a novel probe protein, for a protein with known biological function, or for an existing protein whose mechanism of action is unknown.


Human Protein Entries 19,331
  Protein-Protein Interactions 16,443
  Accuracy(%) 83.9
C.elegans Protein Entries 2,860
  Protein-Protein Interactions 4,011
  Accuracy(%) 76.0
Drosophila Protein Entries 2,388
  Protein-Protein Interactions 21,999
  Accuracy(%) 78.1
Yeast Protein Entries 15,213
  Protein-Protein Interactions 15,517
  Accuracy(%) 81.8

  • 2006.5 SPPS launched
  • 2006.5 SPPS Database Updated
  • 2006.6 Human Model was added
  • 2006.8 Drosophila Model was added
  • 2006.9 C.elegans Model was added
  • 2006.11 Yeast Model was added
  • 2006.12 Database Updated
  • 2007.1 Indirect Interaction was added
  • 2008.1 Database Updated
  • 2009.3 Database Updated
  • 2010.1 Database Updated

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