Fragment Search

Rank Fragments by Similarity Score

This example shows to inquire similar fragment motifs from a library.

Coil fragment of 1DUR-A (15-25): Table  II shows  the  image  of protein 1DURA  (PDB  ID) and  its motif of coil fragment  of 1DUR-A  (15-25).  The sequence and PFSC express of motif are list  on  the  right  site.  The PFSC code indicates that the fragment of 1DUR-A (15-25) has alike alpha-helix at N-terminal to connect alike beta-strand at C-terminus.

In order to show the capability of protein fragment search by PFSC approach, a library with diverse homology was constructed.  The structure of 1DURA (PDB ID) on each hierarchal level belongs to protein of Ferredoxin II, family of Short-chain ferredoxins, fold of Ferredoxin-like and class of alpha+beta.  According hierarchy of 1DURA (PDB ID), a library of 100 proteins with diverse degrees for  structural  homology  was  constructed.  Table  III  shows  the  images  and  names  of PDB ID which categorized by Structure Classification of Protein (SCOP), such as family protein like, super-family protein-like, fold protein-like, protein belong to class alpha+beta, all alpha, all beta and alpha/beta.

Results and similarity score: The fragments with structural similarity to1DUR-A (15-25) are ranked by PFSA-S. Part of top results is displayed in below table. All PFSA-S value is plotted in Fig. 2.

Top four of motifs: Table VI displays four of proteins and motifs with top score PFSA-S.  It is significant that all characteristics for each motif are expressed and associated by one-dimensional strings. The one-dimensional digitized description benefits for computer in high throughput of mass of data with quantitative assessment of similarity, including comparison  of PFSC,  sequence, size of side chain of amino acid and physicochemical properties of each residue.