SynLinker: an integrated system for designing linkers and synthetic fusion proteins

Bioinformatics. 2015 Nov 15;31(22):3700-2. doi: 10.1093/bioinformatics/btv447. Epub 2015 Jul 29.


Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins.

Availability and implementation: SynLinker is freely available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Databases, Protein
  • Humans
  • Recombinant Fusion Proteins / chemical synthesis*
  • Software*
  • User-Computer Interface


  • Recombinant Fusion Proteins