Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region

In multi-domain proteins, the domains are connected by a flexible unstructured region called as protein domain linker. The accurate demar-cation of these linkers holds a key to understanding of their biochemical and evolutionary attributes. This knowledge helps in designing a suit-able linker for engineering stable multi-domain chimeric proteins. Here we propose a novel method for the demarcation of the linker based on a three-dimensional protein structure and a domain definition. The pro-posed method is based on biological knowledge about structural flexibility of the linkers. We performed structural analysis on a linker probable re-gion (LPR) around domain boundary points of known SCOP domains. The LPR was described using a set of overlapping peptide fragments of fixed size. Each peptide fragment was then described by geometric in-variants (GIs) and subjected to clustering process where the fragments corresponding to actual linker come up as outliers. We then discover the actual linkers by finding the longest continuous stretch of outlier frag-ments from LPRs. This method was evaluated on a benchmark dataset of 51 continuous multi-domain proteins, where it achieves F1 score of 0.745 (0.83 precision and 0.66 recall). When the method was applied on 725 con-tinuous multi-domain proteins, it was able to identify novel linkers that were not reported previously. This method can be used in combination with supervised / sequence based linker prediction methods for accurate linker demarcation.