Biomolecular Modelling

Vakinformatie

Biomolecular modelling

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G79AE.htm

Examenvragen

Exam of 21/01/2020

1. Describe the different methods for structure prediction and explain in which situation they are used.

2. Differences and similarities between genetic algorithms and monte carlo simulated annealing.

3. You have a set of molecules able to bind a target, but they can not be used as drugs. There is a database of drug-like compounds. You have the structure of the active ligands, of the target but not of the complex. What would you do to find new drugs

4. Rndom question: describe the steps of moelcular dynamics

5. True or false questions:

       a. The PDB is the best format to store data of protein-ligand complexes 
       b. FF for small molecules can not be used for proteins
       c. The first step of conjugate gradient is steepest descent

Exam of 20/01/2020

1. (Oral) Describe Monte Carlo simulation and what it is used for.

2. (Oral)Random question: explain the enrichment factor.

3. What is a scoring function and which types are there?

4. You have a set of molecules able to bind a target, but they can not be used as drugs. There is a database of drug-like compounds. You have the structure of the active ligands, of the target but not of the complex. What would you do to find new drugs

5. 4 true or false questions:

      a. All FF should have a term for hydrogen bonds.
      b. Molecular dynamics is the best method to predict the structure of a protein.
      c. The first step in the conjugated gradient method is the same as in the steepest descent.
      d. The goal of the lead optimization phase is to increase the potency of the molecule.