Peptide reagent design based on physical and chemical properties of amino acid residues

: It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so-called AABPD (amino acid based-peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three-dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the ph...

• Type: Journal
• Year: 2007
• Where: JCC
• Authors: Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang, Kuo-Chen Chou
• Keywords: Amino Acid Position, Amino Acids, JCC 2007, Peptides