薛定谔教程--Glide分子对接 | Ligand Docking

薛定谔教程–Glide分子对接 | Ligand Docking

Ligand Docking功能模块

Ligands

1. Receptor grid:From file 上传受体文件形式
2. Use ligands from: 上传配体的形式
3. Use input partial charges 限制上传配体条件
   • Do not dock or score ligands with more than:500 atoms
   • Do not dock or score ligands with more than:100,rotatable bonds
4. Scaling of van der Waals radi 调节受体范德华半径缩放比例

Setting对接准确性和采样的设置

1. Precision:
   • SP(standard precision)
   • HTVS (high throughput virtual screening) 高通量筛选，快速筛选小分子，比如数据库
   • XP(extra precision)
   • SP-Peptide
2. Ligand sampling: Flexible 配体取样，配体的柔性
   • Sample nitrogen inversions 氮反转采样
   • Sample ring conformations 成环采样
     • Sample macrocycles using Prime. 使用Prime采样大环 Non-macrocycle ligands will be skipped.
     • Include input ring conformation包括输入环构象
   • Bias sampling of torsions for：扭转采样
     • All predefined functional groups所有预定义的官能团
     • Amides only: 酰胺结合 Penalize nonplanar conformation
3. Add Epik state penalties to docking score将EPIK的处罚添加到对接得分
4. Reward intramolecular hydrogen bonds
5. Enhance planarity of conjugated pi groups
6. Apply |Large excluded volumes penalties
7. Show excluded volumes
8. Advanced Settings…

output 输出