Free Molecular Docking Certification Assessment - StemSkills Lab
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Free Molecular Docking Certification Assessment

StemSkills Lab > Free Molecular Docking Certification Assessment

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