The continuous advancement in molecular biology and information technology aided the development of a rich molecular simulation repertoire that can be applied in system biology, proteomics, molecular biology, bioinformatics, and materials science. We attempt to introduce the latest developments in drug design based on computational techniques, including protein structure modeling, docking, binding site prediction, quantitative structure–activity relationship (QSAR), and molecular dynamics simulation. Furthermore, a brief discussion on current docking issues, including accuracy of protein structure and protein–ligand interaction, is also included. Weight equation and rules and a new concept on flexibility are also described here as possible solution for these issues.
JOURNAL OF THE CHINESE INSTITUTE OF CHEMICAL ENGINEERS, V.41(6):623–635.