Molecular Dynamics and Structure Refinement Quiz

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Which type of functional group has the greater propensity to act as an acceptor in intermolecular interactions?

Carbonyl groups

Ester groups (correct)

Ether groups

Hydroxyl groups

What are 3D pharmacophores used for?

Identification of compounds with 2D properties

Identification of compounds with high biological activity

Identification of compounds with similar chemical structures

Identification of compounds with 3D properties (correct)

What is the purpose of 3D pharmacophore searching?

To identify structures with high biological activity

To identify structures with high solubility

To identify structures with desired activity (correct)

To identify structures with similar chemical structures

What is the first stage in the two-stage procedure for 3D database searching?

Rapid screening Signup and view all the answers

What is the purpose of conformational analysis?

To identify all accessible minimum-energy structures Signup and view all the answers

Which type of function is used to score and rank different members of the population in the GASP algorithm?

Fitness function Signup and view all the answers

What is the structure of the chromosome in GASP?

2N - 1 bitstrings Signup and view all the answers

What does each binary string in the chromosome represent in GASP?

Torsion angle values Signup and view all the answers

How are new members of the population generated in GASP?

Crossover and mutation Signup and view all the answers

What does the mutation operator involve in GASP?

Flipping a bit or altering the value of an integer Signup and view all the answers

Which method involves generating conformations by systematically assigning values to torsion angles?

Grid search Signup and view all the answers

What is the total number of conformations generated by the grid search if there are 3 variable torsion angles with 3, 2, and 2 values permitted to each, respectively?

12 Signup and view all the answers

Which method involves randomly modifying and minimizing previously generated structures to search for new conformations?

Random conformational search Signup and view all the answers

What is the Metropolis criterion used for in the Metropolis Monte Carlo scheme?

To calculate the Boltzmann factor Signup and view all the answers

What does simulated annealing involve?

Gradual reduction of temperature Signup and view all the answers

Which computational models are required to determine the steric and electronic properties of a molecule?

Both quantum mechanics and molecular simulation Signup and view all the answers

What is the purpose of the CSD and the PDB databases?

To store knowledge and rules about conformational properties Signup and view all the answers

Which technique is commonly used to determine protein structures in the PDB database?

X-ray crystallography Signup and view all the answers

What is the main purpose of comparative modeling (homology modeling)?

To predict the 3D structure of a protein based on its homologous proteins Signup and view all the answers

What type of information can be derived from the CSD database?

All of the above Signup and view all the answers

According to the text, what is a clique in graph theory?

A completely connected subgraph in a graph Signup and view all the answers

What is the purpose of the DISCO program mentioned in the text?

To generate a series of potential solutions Signup and view all the answers

Which method uses a pre-calculated set of low-energy conformations obtained using poling?

Maximum likelihood method Signup and view all the answers

What does the scoring function used in the maximum likelihood method take into account?

Fraction of active molecules that match each class Signup and view all the answers

What is the purpose of genetic algorithms (GAs) mentioned in the text?

To optimize potential solutions Signup and view all the answers

Which process involves deriving a 3D pharmacophore by identifying the pharmacophoric groups in each molecule that will be overlaid in the final pharmacophore?

Pharmacophore mapping using constrained systematic search Signup and view all the answers

Which method solves Newton’s equations of motion for the atoms in the system, to give a trajectory that defines how the positions of the atoms vary with time?

Molecular dynamics Signup and view all the answers

Which objective is to determine the 3D pharmacophore(s) that contains the largest number of features common to all of the active molecules, and where these common features can be presented by each molecule in a low-energy conformation?