|
1
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|
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2
|
- Predicting the binding affinity between a target and a ligand forming a
non-covalent complex is a very challenging task that has been pursued
for decades.
- Computer-aided structure-based methods are aimed at predicting the
binding mode of a ligand in the binding site of a protein or any
molecular target and at obtaining an estimate of the binding affinity.
- These methods involve two computational steps: docking and scoring.
- .
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3
|
- In the docking step, multiple protein-ligand configurations are
generated.
- Then, a scoring function is used to calculate the affinity between the
receptor and the ligand for each configuration
- Requirements for the scoring function:
- 1) Binding free energies for each configuration need to be estimated
accurately
- 2) A scoring function must be sufficiently fast to be applied in a
docking algorithm.
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4
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5
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6
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7
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8
|
- Theophylline-binding RNA aptamer
- Trypsin and a series of closely related inhibitors
- Influenza virus neuramindase (wild + mutants) and its three inhibitors
|
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9
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10
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11
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12
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13
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14
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15
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16
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17
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18
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19
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Notes
