MD-intro

Molecular docking primarily aims to predict the binding affinity between two molecules, typically a ligand and a target.

• True

• Falsie

A high negative docking score generally indicates a weaker binding interaction.

• True

• False

In molecular docking, the protein usually remains rigid while the ligand is flexible.

• True

• False

The "docking pose" refers to the specific orientation and conformation of the ligand within the receptor binding site.

• True

• False

Molecular dynamics simulations are used to study the time-dependent behavior of molecular systems.

• True

• False

Molecular dynamics simulations can provide insights into protein flexibility and conformational changes.

• True

• False

Redocking a known ligand to its target protein is a common way to validate a docking protocol.

• True

• False

Ligand preparation for docking often involves adding hydrogens and assigning partial charges.

• True

• False

Induced fit refers to a model where the receptor's binding site rigidly accepts the ligand without any conformational changes.

• True

• False

Electrostatic interactions play a negligible role in ligand-receptor binding affinity.

• True

• False