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Molecular Docking Scoring Problems

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Questions and Answers

What type of docking considers both receptor and ligand flexibility?

Semi-flexible ligand docking

Flexible docking (correct)

Rigid body docking

Pseudo-flexible ligand docking

In which type of docking are both partners treated as rigid?

Rigid body docking (correct)

(Pseudo/Semi)-Flexible ligand docking

Unbound docking

Flexible docking

What is the primary goal of 'bound' docking?

Producing a new co-crystallized complex

Reconstructing the original complex of two molecules (correct)

Introducing flexibility in the ligand

Achieving conformational changes in the molecules

What is the critical element in a search procedure according to the text?

Effectiveness in covering relevant conformational space Signup and view all the answers

Which type of docking requires considering the active site of the protein?

Targeted docking Signup and view all the answers

What is the primary difference between bound and unbound docking?

'Bound' docking involves splitting co-crystallized molecules, while 'unbound' uses them as is. Signup and view all the answers

Which type of docking tests the validity of algorithms by reconstructing original complexes?

'Bound' docking Signup and view all the answers

'(Pseudo/Semi)-Flexible ligand docking' mainly focuses on which element being flexible?

'Ligand' Signup and view all the answers

'Grid Generation Construction' is primarily associated with which aspect of molecular docking?

'Blind' docking Signup and view all the answers

'Speed and effectiveness in covering relevant conformational space' are highlighted as critical in which phase of molecular docking?