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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 preferred binding pose and affinity of a ligand in a receptor site
The amino-acid sequence of a receptor
The folding pathway of a protein
The melting temperature 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)
Molecular weight
Alphabetical ligand name
3.
A "search space" (grid box) in docking defines:
The force field version
The color scheme of the output
The number of CPU cores used
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?
.docx
.csv
.fasta
.pdbqt
5.
Preparing a protein for docking typically includes all EXCEPT:
Randomizing the backbone coordinates
Assigning charges
Adding polar hydrogens
Removing water molecules (unless structurally important)
6.
"Blind docking" refers to:
Docking without a computer
Docking only hydrogen atoms
Searching the entire receptor surface when the binding site is unknown
Docking with the ligand hidden
7.
A more negative Vina score generally indicates:
No binding
A larger ligand
Weaker predicted binding
Stronger predicted binding
8.
Treating selected ligand bonds as rotatable during docking accounts for:
Crystallographic resolution
Ligand conformational flexibility
Solvent viscosity
Receptor mutations
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 model quantum effects fully
They approximate affinity and can mis-rank poses
They require no receptor structure
They compute exact free energies
11.
Re-docking a co-crystallized ligand to check that the method reproduces the known pose is called:
Redocking / pose validation (often via RMSD to the crystal pose)
Ensemble docking
Cross-docking
Fragment growing
12.
An RMSD of ≤ 2 Å between a docked pose and the crystallographic pose is usually interpreted as:
A successful reproduction of the native binding mode
An unbound ligand
A failed docking
A covalent bond
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:
Align sequences
Draw 2D structures
Minimize the whole trajectory
Estimate the quality/affinity of each generated pose
15.
Adding Gasteiger charges during ligand prep is used to:
Increase resolution
Assign partial atomic charges for scoring electrostatics
Add water
Change the molecular formula
16.
Exhaustiveness in Vina primarily affects:
The receptor sequence
The output file name
The thoroughness of the conformational search (and runtime)
The temperature
17.
Cross-docking evaluates:
Docking two ligands together
Docking a ligand back into its own crystal structure
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?
Steric clash / van der Waals
Full explicit-solvent entropy from a long simulation
Hydrogen bonding
Hydrophobic contact
19.
Consensus/ensemble docking improves reliability by:
Ignoring the binding site
Using one pose only
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
Sequence alignment
A molecular dynamics simulation of the complex
Gel electrophoresis
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