Free Biomolecular Modeling and Simulations Certification Assessment | StemSkills Lab
Skip to content
See live workshops

Free Biomolecular Modeling and Simulations Certification Assessment

Test your knowledge of biomolecular modeling: homology modeling, solvent models, force fields, and 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.

Biomolecular Modeling and Simulations certification assessment

1
Take the quiz
20 questions on biomolecular modeling and simulations. About 20 minutes, at your own pace. 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:
:
:

Biomolecular Modeling and Simulations 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.
Homology (comparative) modeling builds a 3D model using:
Only the target sequence with no templates
A related protein of known structure as a template
A DNA gel
A mass spectrum
2.
A prerequisite for reliable homology modeling is:
Sufficient sequence identity to a suitable template (generally higher = better)
No alignment
0% sequence identity to any known structure
A random template
3.
The Protein Data Bank (PDB) primarily stores:
Codon usage
Reaction kinetics tables
Gene expression levels
Experimentally determined 3D biomolecular structures
4.
A Ramachandran plot evaluates:
Solvent density
Ligand affinity
Charge distribution
Backbone φ/ψ dihedral angles (stereochemical quality)
5.
Explicit solvent models water as:
A uniform dielectric constant only
Individual water molecules in the system
A single point charge for the whole box
Vacuum
6.
Implicit solvent (e.g., GB/PB) approximates water as:
A continuum dielectric medium
Ice
A protein
Explicit molecules
7.
Energy minimization finds:
The global maximum energy
The sequence
The melting temperature
A nearby local energy minimum of the structure
8.
A force field in biomolecular simulation is:
A parameterized potential energy function for the molecular system
An alignment score
A microscope
A magnetic device
9.
Which is an example of a common protein force field family?
BLAST
ImageJ
Clustal
AMBER / CHARMM / OPLS / GROMOS
10.
Model validation tools (e.g., PROCHECK/MolProbity) primarily assess:
mRNA levels
Stereochemical/geometry quality of a structure or model
Gene function
Ligand solubility
11.
SASA (solvent-accessible surface area) quantifies:
The number of chains
The timestep
The net charge
How much surface is exposed to solvent
12.
Coarse-grained models (e.g., MARTINI) improve efficiency by:
Using quantum mechanics for all atoms
Grouping several atoms into single interaction beads
Adding more atoms
Removing the force field
13.
Quantum mechanics/molecular mechanics (QM/MM) is used when:
No chemistry occurs
The protein is ignored
Only water matters
Part of the system (e.g., a reaction center) needs quantum treatment while the rest is classical
14.
Loop modeling is often the hardest part of homology modeling because loops:
Are variable/flexible and poorly conserved between template and target
Contain no atoms
Are always helical
Never contact solvent
15.
A multiple sequence alignment (MSA) contributes to modeling by:
Measuring temperature
Removing water
Setting the barostat
Identifying conserved residues and guiding template/target alignment (and contacts)
16.
Which statement about simulation timescales is correct?
All biological processes occur within 1 fs
MD can always reach seconds trivially
Many functional motions exceed typical all-atom MD reach, motivating enhanced sampling
Timescale is irrelevant
17.
Enhanced-sampling methods (e.g., metadynamics, REMD) aim to:
Overcome energy barriers and sample rare events more efficiently
Slow down sampling
Fix the sequence
Delete the solvent
18.
Free-energy methods (e.g., FEP, MM/PBSA) are used to estimate:
Relative/absolute binding or solvation free energies
The crystal color
The gene promoter
The camera angle
19.
A key reason to run replicas or repeat simulations is to:
Waste compute deliberately
Assess reproducibility and statistical significance of observations
Avoid any analysis
Change the force field mid-run
20.
Before trusting any model or simulation result, a good practice is to:
Ignore the force field
Publish immediately
Validate against experimental data and check convergence/quality metrics
Remove all hydrogens
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