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Keywords:

  • PQSA-Pred;
  • SMART;
  • FunD composition;
  • PseAA composition;
  • complexity measurement factors;
  • nearest neighbor algorithms;
  • jackknife test

In vivo, some proteins exist as monomers (single polypeptide chains) and others as oligomers. The latter are composed of two or more chains (subunits) that are associated with each other through noncovalent interactions and, occasionally, disulfide bonds. Oligomers can be further classified into homo-oligomers (formed by identical subunits) and hetero-oligomers (formed by different subunits), and they form the structural basis of various biological functions such as cooperative effects, the allosteric mechanism and ion-channel gating. Therefore, it would be of less interest or of low priority for crystallographic scientists to crystallize a single protein chain and determine its three-dimensional structure if it is already known as part of an oligomer. However, it is both time-consuming and laborious to acquire such information on the quaternary structure attribute purely by experiment. In particular, with the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop an automated method by which crystallographic scientists can rapidly and effectively identify which quaternary attribute a particular protein chain has according to its sequence information. In view of this, a computational method has been developed by hybridizing the approaches of functional domain composition and pseudo amino acid composition. For the convenience of crystallographic scientists, a user-friendly web server, PQSA-Pred, has been established at http://218.65.61.89:8080/bioinfo/pqsa-pred, by which the desired information can be easily obtained.