A Konowledge-based Protein Modeling System and Its Evaluation III. A Sensitive Method for Evaluation Protein Model.
A new scoring table of compatibilities of residues with environments in a protein has been derived from environment-dependent amino acid substitution tables. The environments of the residues in the 3D structure are described by: (1) the secondary structure; (2) the solvent accessibility; (3) the hydrogen bonding. On the basis of the scoring table, an assessment method of protein models is proposed. Compared with the famous software Profile-3D, The method not only shows a more effective test of the accuracy of a 3D protein model, but also exhibits a higher sensitivity to the local misfolding. It is an important module in our protein modeling system PMODELING.
Zhang
Bao-Hong
BH
Shanghai Institute of Biochemistry, Academia Sinica, Shanghai 200031, China.
Ding
Da-Fu
DF