Chengcheng Liu1, Ju Xin Chin1, Dong-Yup Lee2. 1. Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore. 2. 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.
Abstract
UNLABELLED: 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 http://bioinfo.bti.a-star.edu.sg/synlinker. CONTACT: cheld@nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: 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 http://bioinfo.bti.a-star.edu.sg/synlinker. CONTACT: cheld@nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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