Quiz lecture 9

What shape is the energy landscape of an amino acid sequence with folding ability toward a folded structure?

• Flat

• Rugged

• Funnel-shaped

• Spherical

What method treats protein sequence design as an energy optimization problem?

• ProteinMPNN

• Rosetta

• Deep learning models

• Computational filtering

What does ProteinMPNN utilize to improve its model?

• Sequence similarity above 70%

• Categorical cross-entropy loss per residue

• Random decoding order

• Backbone building

What is the main objective of using RFdiffusion in protein design?

• To maximize protein size

• To minimize protein diversity

• To generate endlessly diverse outputs

• To simplify protein synthesis

How does RFdiffusion create new protein structures?

• By refining random noise into realistic structures

• By following a fixed left-to-right decoding order

• By predicting amino acids based on energy levels

• By copying sequences from existing proteins

What role does self-conditioning play in RFdiffusion's training?

• It decreases model accuracy

• It enhances prediction accuracy by considering previous steps

• It simplifies the model architecture

• It increases the diversity of the outputs

What indicates a successful design by ProteinMPNN and RFdiffusion?

• High sequence recovery rate

• Low sequence recovery rate

• Minimal energy consumption

• Simplistic design models

What is a key advantage of RFdiffusion over existing methods for protein design?

• It requires extensive expert customization

• It only focuses on small proteins

• It quantitatively outperforms existing methods across a broad range of tasks

• It has a lower success rate in computational and experimental validations

RFdiffusion models are fine-tuned from which structure prediction network?

• AlphaFold

• RoseTTAFold

• ESMFold

• OmegaFold

What determines the folding ability of a protein to a particular tertiary motif according to Go's consistency principle?

• The precise sequence of amino acids

• The overall shape of the protein

• The lengths of secondary structures and the connecting loops

• The number of hydrophobic amino acids present