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