181 Lec - PPT2

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

Quantum mechanics

Molecular simulation

Both quantum mechanics and molecular simulation (correct)

Neither quantum mechanics nor molecular simulation

What is the purpose of the CSD and PDB databases in the field of molecular structures?

To store experimental data only

To determine bond lengths and conformations of specific molecular fragments

To derive 3D pharmacophores

To provide knowledge and rules about conformational properties and intermolecular interactions (correct)

What is the main purpose of the PDB database?

To store x-ray structures of organic and organometallic compounds

To determine bond lengths and conformations of specific molecular fragments

To provide information about intermolecular interactions

To form the basis of comparative modeling (correct)

Which type of functional group is more likely to act as an acceptor in intermolecular interactions?

Ester groups Signup and view all the answers

What is the purpose of 3D pharmacophore searching?

To identify compounds with 3D properties Signup and view all the answers

What is the purpose of pharmacophore features in drug design?

To specify the spatial relationships between features Signup and view all the answers

What is the purpose of rapid screening in 3D database searching?

To eliminate molecules that do not match the query 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 is a clique in graph theory?

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

Which method generates a series of low-energy conformations for each molecule?

DISCO program Signup and view all the answers

What is the scoring function used in the Maximum Likelihood Method for pharmacophore mapping?

$M summation till K+1$ Signup and view all the answers

Which of the following is true about the fitness function in the GASP algorithm?

It ranks different members of the population Signup and view all the answers

What is the chromosome structure in the GASP algorithm?

2N - 1 bitstrings Signup and view all the answers

How are new members of the population generated in the GASP algorithm?

Crossover and mutation Signup and view all the answers

What is the role of the genetic operators in the GASP algorithm?

To generate new members of the population 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

Which method involves randomly modifying a previously generated structure and then minimizing it?

Random conformational search Signup and view all the answers

What is the criterion used in the Metropolis Monte Carlo scheme for selecting a new structure?

The Boltzmann factor must be larger than a random number 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 a 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 enzyme in Mycobacterium tuberculosis was chosen as the drug target for computer-aided drug discovery and development approaches?

BioA aminotransferase Signup and view all the answers

What is the objective of deriving a 3D pharmacophore in drug discovery?

To identify the 3D pharmacophore that contains the largest number of features common to all of the active molecules Signup and view all the answers