Free Molecular Docking Certification Assessment | StemSkills Lab
Skip to content
See live workshops

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. A 20-minute timer runs once you start. No sign-up needed to start.
2
Sign in to see your result
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.
time left:
:
:

Molecular Docking Certification Assessment

Submit quiz
Once you submit, you will no longer be able to change your answers. Are you sure you want to submit the quiz?
Cancel Submit

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 melting temperature of a protein
The preferred binding pose and affinity of a ligand in a receptor site
The amino-acid sequence of a receptor
2.
AutoDock Vina's default output ranks poses primarily by:
Molecular weight
Predicted binding affinity (kcal/mol, most negative first)
Number of rotatable bonds
Alphabetical ligand name
3.
A "search space" (grid box) in docking defines:
The 3D region of the receptor where the ligand is sampled
The number of CPU cores used
The color scheme of the output
The force field version
4.
Which file format is commonly required for AutoDock/Vina receptor and ligand input?
.fasta
.docx
.csv
.pdbqt
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
Stronger predicted binding
A larger ligand
No binding
8.
Treating selected ligand bonds as rotatable during docking accounts for:
Receptor mutations
Ligand conformational flexibility
Crystallographic resolution
Solvent viscosity
9.
Rigid-receptor docking assumes:
Water is explicitly modeled
The ligand is rigid
The receptor conformation is fixed during the search
No scoring function is used
10.
Which is a common LIMITATION of docking scoring functions?
They model quantum effects fully
They compute exact free energies
They require no receptor structure
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)
Fragment growing
Ensemble docking
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
A covalent bond
An unbound ligand
A failed docking
13.
Which software is a widely used open-source docking engine?
Microsoft Excel
VMD
BLAST
AutoDock Vina
14.
The role of a "scoring function" in docking is to:
Align sequences
Estimate the quality/affinity of each generated pose
Minimize the whole trajectory
Draw 2D structures
15.
Adding Gasteiger charges during ligand prep is used to:
Add water
Change the molecular formula
Increase resolution
Assign partial atomic charges for scoring electrostatics
16.
Exhaustiveness in Vina primarily affects:
The output file name
The thoroughness of the conformational search (and runtime)
The temperature
The receptor sequence
17.
Cross-docking evaluates:
Docking a ligand into a receptor conformation it was NOT co-crystallized with
Docking two ligands together
Docking without a grid
Docking a ligand back into its own crystal structure
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:
Combining multiple scoring functions and/or multiple receptor conformations
Removing all hydrogens
Using one pose only
Ignoring the binding site
20.
After docking, a common NEXT step to test pose stability is:
Gel electrophoresis
Sequence alignment
A molecular dynamics simulation of the complex
PCR
Submit quiz
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • 8
  • 9
  • 10
  • 11
  • 12
  • 13
  • 14
  • 15
  • 16
  • 17
  • 18
  • 19
  • 20
Ready to go beyond the assessment?
Our live, mentor-led cohort takes you hands-on through protein modelling, docking and molecular dynamics, finishing with a project you build yourself and can show on your CV and applications.

See the live cohort

See live workshops