APPLICATION OF THE DEAD-END-ELIMINATIOD TO SOLVE THE SIDE CHAIN FLEXIBILITY PROBLEM IN MOLECULAR DOCKING
应用死端排除法考虑分子对接中的侧链柔性

that the dose packing in the interface of molecular docking is similar to that in the interior of proteins. Therefore, mothods applied to the prediction of side chain conformation in proteins such as the dead-end-elimination method can also be applied to the prediction of side chain conformation in the inteface of molecular docking . This assumption has ho tested by using 9 crystal structures. The results show that the assumption is basically correct. Application 2 Crystal structures of proteases and their corresponding inhibitors was rather successful. Out of 9 ligand structures, 7 structures had the correct trend in root-mean -square deviation. The authors also discoved that flexibility of the receptor structures is rela tively samll. Hence, the conformational change owing to the close packing in the interface is very small. Based on these results, the authors propose a new proedure for molecular docking,namely, after rigid body docking the prediction of the side chain conformation of the amino acid residues is added inhibitor complex structure shows that the signal to noise ratio has increased for the correct solution in molecular docking, relative to the wrong solutions.