Patent ID: 7212924
Filing Date: 2007-05-01
Classification: C07K,G01N,G16B

Abstract:
1. A method of predicting a scaffold of a protein comprising a query sequence, wherein said method uses a database which contains environmental information on the side chain of each amino acid residue contained in the amino acid sequence of each reference protein whose three-dimensional structure is known or predictable, wherein the amino acid sequence of each of the reference proteins is divided into two or more core segment sequences comprising two or more contiguous amino acid residues based on the characteristics of the three-dimensional structure of the reference protein, wherein the amino acid sequence of each of the reference proteins is divided into two or more core segment sequences which are predetermined to form a hydrophobic core, and into one or more sub segment sequences which are not predetermined to form a hydrophobic core, and wherein said method comprises: conducting matching based on the environmental information on each amino acid residue of each of the two or more core segment sequences of the reference protein and hydrophobicity or hydrophilicity property of the side chain of each amino acid residue of the query sequence, and wherein the matching is performed by sliding the two or more core segment sequences of the reference protein on the query sequence without consideration of any gaps except those at one end or both ends of the core segment sequence, and choosing at least one template protein among the reference proteins that has highest similarity in three-dimensional structure to the protein comprising the query sequence based on the matching score of the whole sequence and predicting the scaffold of the protein comprising a query sequence.