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Molecular Docking — Free Certification Assessment

StemSkills Lab > Molecular Docking — Free Certification Assessment

Molecular Docking — Free Certification Assessment

Test your knowledge of molecular docking — AutoDock/Vina, binding poses, scoring, and validation. Pass at 70% to earn a verifiable StemSkills certificate you can download as a PDF and add to your LinkedIn profile. Free.

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Molecular Docking — Certification Assessment

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Free certification assessment. Pass at 70% to earn a verifiable StemSkills certificate.

  • Questions count: 20
  • Passing grade: 70%
  • Time limit: 20 minutes
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1.
In molecular docking, the primary goal is to predict:
The amino-acid sequence of a receptor
The preferred binding pose and affinity of a ligand in a receptor site
The melting temperature of a protein
The folding pathway of a protein
2.
AutoDock Vina's default output ranks poses primarily by:
Number of rotatable bonds
Predicted binding affinity (kcal/mol, most negative first)
Alphabetical ligand name
Molecular weight
3.
A "search space" (grid box) in docking defines:
The 3D region of the receptor where the ligand is sampled
The color scheme of the output
The number of CPU cores used
The force field version
4.
Which file format is commonly required for AutoDock/Vina receptor and ligand input?
.docx
.csv
.pdbqt
.fasta
5.
Preparing a protein for docking typically includes all EXCEPT:
Assigning charges
Adding polar hydrogens
Removing water molecules (unless structurally important)
Randomizing the backbone coordinates
6.
"Blind docking" refers to:
Docking with the ligand hidden
Docking without a computer
Docking only hydrogen atoms
Searching the entire receptor surface when the binding site is unknown
7.
A more negative Vina score generally indicates:
No binding
A larger ligand
Stronger predicted binding
Weaker predicted binding
8.
Treating selected ligand bonds as rotatable during docking accounts for:
Solvent viscosity
Crystallographic resolution
Ligand conformational flexibility
Receptor mutations
9.
Rigid-receptor docking assumes:
The receptor conformation is fixed during the search
Water is explicitly modeled
No scoring function is used
The ligand is rigid
10.
Which is a common LIMITATION of docking scoring functions?
They model quantum effects fully
They require no receptor structure
They compute exact free energies
They approximate affinity and can mis-rank poses
11.
Re-docking a co-crystallized ligand to check that the method reproduces the known pose is called:
Fragment growing
Cross-docking
Ensemble docking
Redocking / pose validation (often via RMSD to the crystal pose)
12.
An RMSD of ≤ 2 Å between a docked pose and the crystallographic pose is usually interpreted as:
A failed docking
A covalent bond
An unbound ligand
A successful reproduction of the native binding mode
13.
Which software is a widely used open-source docking engine?
BLAST
AutoDock Vina
VMD
Microsoft Excel
14.
The role of a "scoring function" in docking is to:
Estimate the quality/affinity of each generated pose
Draw 2D structures
Align sequences
Minimize the whole trajectory
15.
Adding Gasteiger charges during ligand prep is used to:
Add water
Increase resolution
Change the molecular formula
Assign partial atomic charges for scoring electrostatics
16.
Exhaustiveness in Vina primarily affects:
The thoroughness of the conformational search (and runtime)
The receptor sequence
The output file name
The temperature
17.
Cross-docking evaluates:
Docking without a grid
Docking a ligand back into its own crystal structure
Docking two ligands together
Docking a ligand into a receptor conformation it was NOT co-crystallized with
18.
Which factor is NOT directly represented in most fast empirical docking scores?
Full explicit-solvent entropy from a long simulation
Hydrophobic contact
Hydrogen bonding
Steric clash / van der Waals
19.
Consensus/ensemble docking improves reliability by:
Removing all hydrogens
Using one pose only
Combining multiple scoring functions and/or multiple receptor conformations
Ignoring the binding site
20.
After docking, a common NEXT step to test pose stability is:
A molecular dynamics simulation of the complex
Gel electrophoresis
PCR
Sequence alignment
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