| 학회 |
한국공업화학회 |
| 학술대회 |
2021년 봄 (05/12 ~ 05/14, 부산 벡스코(BEXCO)) |
| 권호 |
25권 1호 |
| 발표분야 |
포스터-생물공학 |
| 제목 |
Effect of ligand torsion number on the prediction of protein-ligand binding affinity |
| 초록 |
Ligand torsion number is related to the flexibility of ligand, and generally incorporated as a crucial variable in the thermodynamic function of binding free energy. In this study, we investigated how the ligand torsion number has influence on the binding affinity prediction of AutoDock, a popular molecular docking simulation tool. The pKd values of various protein-ligands were estimated by using the binding free energy function of AutoDock and compared with their experimental pKd values. The torsion number dependent comparison showed that the predicted binding affinities were mostly underestimated in the complexes of higher torsion numbers, whereas the underestimated and overestimated cases were relatively balanced at relatively lower torsion numbers. A new weight factor for torsion free energy term of binding energy function was determined and introduced to make correction to the underestimation of binding affinity of ligands with high torsion numbers. |
| 저자 |
Dinesh Kumar Sriramulu, 이선구
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| 소속 |
부산대 |
| 키워드 |
Protein-ligand interactions; Binding energy; AutoDock
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| E-Mail |
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