Free Protein-Protein Modeling Certification Assessment | StemSkills Lab
Skip to content
See live workshops

Free Protein-Protein Modeling Certification Assessment

Test your knowledge of protein-protein modeling: interfaces, HADDOCK, hot spots, and CAPRI metrics. Pass at 70% to earn a verifiable StemSkills certificate. Download it as a PDF and add it to your LinkedIn profile. It is free.

Protein-Protein Modeling certification assessment

1
Take the quiz
20 questions on protein-protein modeling. 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:
:
:

Protein-Protein Modeling 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.
Protein–protein docking predicts:
The DNA sequence of a gene
How two proteins assemble into a complex (relative orientation/interface)
The codon usage
The melting temperature
2.
A protein–protein "interface" refers to:
The GUI of the software
The set of residues in contact between the two partners
The solvent box
The force field file
3.
HADDOCK is notable for being a:
Rendering engine
Force field
Sequence aligner
Data-driven docking approach that uses experimental/ predicted restraints
4.
"Shape complementarity" at an interface describes:
Geometric fit between the two protein surfaces
The same secondary structure
Identical sequences
Equal molecular weights
5.
Rigid-body protein–protein docking initially treats each protein as:
A flexible chain sampled residue-by-residue
A single atom
A rigid object, sampling relative translations/rotations
A DNA duplex
6.
"Induced fit" at a protein–protein interface means:
Conformational changes occur upon binding
Only water binds
The interface never changes
The sequence mutates
7.
Buried surface area (BSA) upon complex formation is used to:
Characterize interface size/extent of burial
Assign charges
Count chains
Measure temperature
8.
A common scoring signal for a plausible PPI model is:
Zero contacts
Favorable shape + electrostatic/hydrophobic complementarity with few clashes
Maximum steric clash
Random orientation
9.
Which experimental data most directly informs restraint-based PPI docking?
Codon bias
Gene expression microarray
Mutagenesis/cross-linking/NMR data on interface residues
Ligand solubility
10.
"Hot spot" residues at an interface are:
Residues far from the interface
Only glycines
A few residues contributing disproportionately to binding energy
Buried metal ions
11.
Homodimer vs heterodimer differ in that a homodimer has:
Two identical protein chains
Only DNA
Two different proteins
No interface
12.
A major challenge in protein–protein docking (vs small-molecule docking) is:
Large, flat interfaces and backbone flexibility of both partners
There is never any interface
Ligands are too small
No scoring is possible
13.
FFT-based docking (e.g., ZDOCK-style) accelerates the search by:
Ignoring the receptor
Efficiently scanning translations/rotations via correlation in Fourier space
Aligning sequences
Running MD only
14.
Refinement of a docked complex often uses:
PCR
Energy minimization / short MD and interface side-chain repacking
Gel filtration
Sequence trimming
15.
Co-evolution / coupled mutations between two proteins can indicate:
No relationship
Residue pairs likely in contact at the interface
The expression host
The melting point
16.
An "encounter complex" in PPI refers to:
Transient early-association states before the final bound complex
A ligand pose
A denatured protein
The final crystal structure
17.
Which metric assesses a predicted complex against a reference (CAPRI-style)?
BLAST e-value
Interface RMSD / ligand RMSD / fraction of native contacts (fnat)
Codon adaptation index
Tm
18.
Electrostatic steering in association means:
Only van der Waals matters
Long-range electrostatics can guide partners toward the correct orientation
Charges are ignored
Water is removed
19.
AlphaFold-Multimer / deep-learning complex prediction primarily leverages:
Gel electrophoresis
Evolutionary/co-evolution signals + learned structural patterns
Explicit-solvent MD only
Manual docking only
20.
After predicting a complex, a reasonable validation is to check:
The gene promoter
The ligand's molecular weight only
Interface plausibility, clash score, and stability under short MD
The PCR cycle number
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