Free Biomolecular Modeling and Simulations Certification Assessment | StemSkills Lab
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Free Biomolecular Modeling and Simulations Certification Assessment

StemSkills Lab > Free Biomolecular Modeling and Simulations Certification Assessment

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