Quantum mechanical scoring for protein docking.
We develop a docking protocol based on quantum mechanical/molecular mechanical calculations in which quantum mechanical energy is used as scoring. We test the protocol with three groups of examples with various binding site characteristics. The new docking method performs as well as or better than conventional docking methods in all three groups. In particular, for proteins with primarily hydrophobic binding sites, structural motifs with possible pi-pi interactions are often found and it is shown that these can be better modeled with quantum mechanical scoring docking than force field based methods. It seems that the new method performs in such cases to a great accuracy.
Cho
Art E
AE
Department of Biotechnology and Bioinformatics, Korea University, Jochiwon, Chungnam 339-700, Republic of Korea. artcho@korea.ac.kr
Chung
Jae Yoon
JY
Kim
Minsup
M
Park
Kichul
K
D001554:Benzene / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D019281:Dimerization; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008670:Metals / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D011789:Quantum Theory; D013816:Thermodynamics
D008024:Ligands; D008670:Metals; D011506:Proteins; D001554:Benzene