title: SynLinker: an integrated system for designing linkers and synthetic fusion proteins.
abstract: 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.
  
  
  METHODS
  SynLinker is freely available at http://bioinfo.bti.a-star.edu.sg/synlinker.
  
  
  BACKGROUND
  cheld@nus.edu.sg
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Liu
authors.affiliation: Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore.
authors.forename: Ju Xin
authors.initials: JX
authors.lastname: Chin
authors.affiliation: Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore, Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D030562:Databases, Protein; D006801:Humans; D011993:Recombinant Fusion Proteins / Q000138:chemical synthesis*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011993:Recombinant Fusion Proteins