Free Molecular Docking Certification Assessment | StemSkills Lab
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Free Molecular Docking Certification Assessment

Test your knowledge of molecular docking: AutoDock and Vina, binding poses, scoring functions, and pose validation. Pass at 70% to earn a verifiable StemSkills certificate. Download it as a PDF and add it to your LinkedIn profile. It is free.

Molecular Docking certification assessment

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