Paired as Fab
According the numbering of H1, H2, H3, L1, L2 and L3 in the table, we can get the conserved conformation of hypervariable loops of new antibodies.
• • • •
2. 分子对接的方法和结果评价
Molecular docking (Zdockpro in Insight II): • Zdock is a rigid-body, initial stage protein-protein docking algorithm that applies the ligand rotation and the shape complementarity method through the Fast Fourier Transform method (FFT). The ZDOCK scoring function in this release is based on pairwise shape complementarity (PSC). • Rdock is based on the CHARMm simulations program and is usedfor further refinement of poses generated by ZDOCK. It also ranks the docked structures based on the CHARMm electrostatic interaction energy and ACE desolvation energy. Result filtration • Known key amino acid included in or excluded from the resultant interface • Known interaction force: hydrophobic, salt,…
Molecular simulation and dynamics for Structural biology
分子模拟和分子动力学在结构生物 学中的应用
生命科学学院，厦门大学 Shaowei Li，李少伟 2016-5-9
第四届国际分子模拟与信息技术应用学术会议
1.分子对接在中和表位分析中的应用
内容提要
1. 抗体Fab片段模拟的方法 2. 分子对接的方法和结果评价 3. 中和表位的预测和实验验证
(1)H5N1广谱中和表位的预测
(2)HPV6&11交叉中和表位的预测
抗体序列
PDB 抗原 结构
模拟抗体结构
抗原抗体对 接结构模型
模型筛选、优 化、序列比对
保守中和表位
抗病毒多肽片段或模型
1. 抗体Fab片段模拟的方法
2. 分子对接的方法和结果评价（续）
Specific distance amino acid as
interface
Interaction energy analysis SAS decrease
Functional base:
wide-type neutralizing antibody sharing same binding site in different
Strቤተ መጻሕፍቲ ባይዱcture of Influenza A virus
HA protein containing the main neutralizing sites and in antigenic drift in recurrent epidemics of influenza.
Comparative Immunology Microbiology and Infectious Diseases, Lee et al., 2008
antigens,
receptor binding site, …
green: crystal structure, red: docking prediction
内容提要
1. 抗体Fab片段模拟的方法 2. 分子对接的方法和结果评价
3. 中和表位的预测和实验验证
(1)H5N1广谱中和表位的预测
(2)HEV中和表位和受体结合位点的预测 (3)HPV6&11交叉中和表位的预测 4. 小结与展望
Neutralization assay of H5N1 virus with a panel of mAb
Neutralization titer of the indicated MAb by class H5N1 virus Ck/HKYU22/02 Ck/IDN/2A/04 Dk/IDN/MS/04 Ck/Salatiga/BBVet1/05 Ck/Malang/BBVet4/04 HK213/03 Ck/Bantul/BBVet1/05 Ck/YN/115/04 Gs/GX/2112/04 Ck/Jogjakarta/BBVet-IX/04 Dk/VNM/283/05 Rb pochard/HK/821/02 Ck/MYS/5858/04 VNM/1194/04 VNM/1203/04 Dk/VNM/N-XX/04 Dk/VNM/S654/05 MDk/JX/1653/05 Dk/FJ/897/05 Gs/GY/337/06 Gs/YN/5539/05 IDN/5/05 BH goose/QH15/05 Gf/ST/1341/06 MDk/JX/2295/05 Ck/HN/999/05 Dk/HN/157/05 Ck/ST/4231/03 Dk/GX/951/05 Dk/HN/1265/05 Ck/GX/2439/04 Qa/Gx/575/05 Common Magpie/HK/645/06 Oriental Magpie Robin/HK/366/06 Clade 20A11 8 2.1 2.1 2.1 2.1 1 2.1 2.4 5 2.1 1 1 1 1 1 1 1 9 9 4 7 2.1 2.2 2.2 2.2 2.3 2.3 2.2 2.3 2.3 5 2.3 2.3 2.3 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 16F13 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 13D4 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 I 16G3 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 14E4 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 20H2 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 3C8 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 ≥3200 ≥3200 1600 ≥3200 ≥3200 ≥3200 < < < < < ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 < 400 ND < II 9H12B 16A12 ≥3200 800 ≥3200 ≥3200 < 1600 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 1600 1600 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < < ≥3200 1600 14D4 ≥3200 ≥3200 < < ≥3200 ≥3200 < < 1G2 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 3F1B8 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 16F8 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 ≥3200 ≥3200 < < < < < < < ≥3200 ≥3200 < < ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 III 4GE1 ≥3200 1600 800 ≥3200 < ≥3200 ≥3200 800 < < ≥3200 ≥3200 < < < < < < < < < 800 800 < ≥3200 < 800 400 ≥3200 ≥3200 < < < < 1D8 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < < < < < < < < < < < < < < ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 800 < < < < 6CF3 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < < 400 < < < < < < < < < < 800 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 < < 10DD2 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 < ≥3200 ≥3200 < < < < < < < < < < < < < 1600 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 ≥3200 800 ≥3200 < < < <