SynLinker

SynLinker identifies candidate linker peptide sequences for designing recombinant fusion proteins to enable appropriate domain connectivity while preserving structural integrity and functional activity.

Key Features:

• Linker database: A compiled set of 2,260 linker peptide sequences derived from natural linkers extracted from non-redundant multi-domain proteins in the Protein Data Bank (PDB) and artificial/empirical linkers sourced from scientific literature and patents.
• Selection and filtering: Supports selection of linker candidates based on specific selection criteria.
• Fusion assembly and structure prediction: Combines a selected linker with two domain structures appended at the N- and C-terminals and enables prediction of a de novo structure for the resultant fusion protein.
• Multi-domain focus: Targets linker identification for recombinant fusion proteins that connect multiple protein domains to maintain structural integrity and functional activity.

Scientific Applications:

• Synthetic fusion protein design: Identification of optimal linker sequences for engineering recombinant fusion proteins.
• Structural biology: Modeling and prediction of linker effects on domain arrangement and structural stability.
• Biotechnology and (bio)pharmaceutical development: Engineering multi-domain proteins for specific functionalities and therapeutic applications.

Methodology:

Compilation of a database of 2,260 linker sequences from natural linkers extracted from non-redundant multi-domain proteins in the Protein Data Bank (PDB) and artificial/empirical linkers from literature and patents; appended selected linkers between two domain structures at the N- and C-terminals and predicted a de novo structure for the fusion protein.