Computational Molecular Microbiology: Protein Structure Validation and Molecular Docking
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Questions and Answers

Which of the following is a protein structure validation program?

  • PROCHECK (correct)
  • SuperPose
  • PubChem
  • Autodock Vina

    • What is the main purpose of molecular docking in the drug discovery process?

  • Predicting protein function of target protein
  • Modeling the interaction between a small molecule and a protein (correct)
  • Assessing the stereochemical quality of a protein structure
  • Establishing physical contacts between two or more protein molecules

    • What type of interactions are involved in protein-protein interactions (PPIs)?

  • Metal-metal interactions and coordination bonds
  • Electrostatic forces, hydrogen bonding, and the hydrophobic effect (correct)
  • Van der Waals forces and dipole-dipole interactions
  • Covalent bonding and ionic interactions

    • Which of the following is a ligand database used in docking programs?

    <p>PubChem (C)</p> Signup and view all the answers

    What is the main purpose of the Human Reference Interactome (HuRI) map?

    <p>To chart interactions between human proteins (C)</p> Signup and view all the answers

    Which type of cellular function is NOT regulated by protein-protein interactions?

    <p>DNA replication (C)</p> Signup and view all the answers

    What do online tools like STRING primarily analyze?

    <p>Protein-protein interactions (B)</p> Signup and view all the answers

    What is the primary function of Gene Ontology (GO)?

    <p>Describing knowledge of three aspects of the biology of the gene/protein (B)</p> Signup and view all the answers

    Which platform is used for Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis?

    <p>(D)</p> Signup and view all the answers

    What type of data can be analyzed using DAVID?

    <p>Differentially expressed genes and proteins (B)</p> Signup and view all the answers

    Which type of interactions are involved in protein-protein interactions (PPIs)?

    <p>Electrostatic forces, hydrogen bonding, and the hydrophobic effect (B)</p> Signup and view all the answers

    What is the main purpose of molecular docking in the drug discovery process?

    <p>Modeling the interaction between a small molecule and a protein (B)</p> Signup and view all the answers

    Which of the following is a ligand database used in docking programs?

    <p>PubChem (A)</p> Signup and view all the answers

    What are examples of protein structure validation programs?

    <p>PROCHECK, ERRAT, Rampage (C)</p> Signup and view all the answers

    What does the Human Reference Interactome (HuRI) map chart?

    <p>Interactions between human proteins (B)</p> Signup and view all the answers

    Which of the following is a type of cellular function regulated by protein-protein interactions?

    <p>Muscle contraction (A)</p> Signup and view all the answers

    What is the main purpose of the Gene Ontology (GO)?

    <p>Describing knowledge of the biology of genes/proteins (C)</p> Signup and view all the answers

    What type of data can be analyzed using DAVID?

    <p>Differentially expressed genes and proteins (B)</p> Signup and view all the answers

    What is the function of the online tool STRING in protein-protein interaction analysis?

    <p>Analyzing known and predicted protein interactions (A)</p> Signup and view all the answers

    What types of cellular functions are regulated by protein-protein interactions?

    <p>Electron transfer, signal transduction, cell metabolism, muscle contraction, membrane transport (D)</p> Signup and view all the answers

    What is the main purpose of the Human Reference Interactome (HuRI) map?

    <p>Charting interactions between human proteins (B)</p> Signup and view all the answers

    What do functional analysis methods help us to gain insight about?

    <p>The biology underlying a list of genes (D)</p> Signup and view all the answers

    What do online tools like STRING primarily analyze?

    <p>Known and predicted protein interactions (B)</p> Signup and view all the answers

    Which platform is used for Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis?

    <p>DAVID (<a href="https://david.ncifcrf.gov/">https://david.ncifcrf.gov/</a>) (A)</p> Signup and view all the answers

    What type of questions can be answered using functional analysis methods?

    <p>Impact of a viral infection on a cell, impact of a drug treatment/stress/protein knockdown, function of differentially expressed genes/proteins in a disease condition, signaling pathways affected by a disease/stress or viral infection. (A)</p> Signup and view all the answers

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