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Complete Conformation Description with PFSC for Protein with Known 3D Structure

For any protein with given 3D structure, Protein Folding Shape Code (PFSC) is able to provide a complete description of conformation, includes regular secondary fragment and irregular tertiary fragment.

The PFSC reveals the feature of conformation in detail. Also, it is better for comparison of protein structures, for study of conformation change involving sequence mutation and protein design etc.

Protein Folding Shape Code (PFSC) is one-dimensional description folding vector for 5 residues. Any protein with given 3D structure is able to be expressed by PFSC code. Along alpha-C backbone in protein, from N-terminal to C-terminal, the folding conformation of entire protein is described by one-dimensional digitized alphabetic letters.

PFSC provides a complete description for protein conformation, includes regular secondary fragment and irregular tertiary fragment. The PFSC assignment of secondary structural fragments is overall agreed with results in PDB. Also it reflects the flexibility of in folding shape and length for secondary structural fragments.  

The PFSC is fingerprint for protein conformation. It is good for protein structure alignment for comparison. Also, it is applied to high-throughput screening a large protein structural data.

Few of samples are displayed in table below which shows the PFSC description and compares with assignment of secondary structure fragment from authors by PDB and other methods.     

Secondary Structure Described in more Detail

 

Description Covers Tertiary Structures

 

Conformation of Protein (PDB ID=2INQ)in PFSC Description

 

Ref: Yang J. Comprehensive description of protein structures using protein folding shape code. Proteins 2008;71.3:1497-1518     

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