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</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</p> Signup and view all the answers

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

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

    What do online tools like STRING primarily analyze?

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

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

    Signup and view all the answers

    What type of data can be analyzed using DAVID?

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

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

    <p>PubChem</p> Signup and view all the answers

    What are examples of protein structure validation programs?

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

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

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

    What type of data can be analyzed using DAVID?

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

    What do online tools like STRING primarily analyze?

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

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