Computational Tools for Protein Active Site Analysis and Ligand Design

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What is the primary goal of computer-aided ligand design methods?

To construct a ligand atom by atom

To determine desirable locations of atoms within the active site (correct)

To assess the shape of the compounds placed in the active site

To place compounds into the active site randomly

Which method constructs a ligand atom by atom?

Sequential buildup method (correct)

Site point connection method

Whole molecule method

Fragment connection method

In which method are fragments positioned and connected using linkers or scaffolds?

Random connection method

Whole molecule method

Fragment location method

Site point connection method (correct)

Which class of techniques combines features of fragment connection and sequential buildup methods, along with bond disconnection strategies?

Random connection method Signup and view all the answers

What is the purpose of whole molecule methods in ligand design?

To assess shape and/or electrostatic complementarity of compounds in the active site Signup and view all the answers

Which method involves determining locations as 'site points' and then placing fragments within the active site to occupy those locations?

Fragment location method Signup and view all the answers

What is the primary purpose of Quantitative Structure Activity Relationships (QSAR)?

To correlate structural molecular properties with functions for a set of similar compounds Signup and view all the answers

What is the main alternative to get a 3D representation of the target in the absence of crystal structures?

Homology modeling Signup and view all the answers

What is the term used for quantitative structure toxicity relationship modeling applied to toxicological data?

Quantitative Structure Toxicity Relationship (QSTR) Signup and view all the answers

Which approach is considered a complementary method to experimental high throughput screening (HTS) in lead identification?

Structure Based Virtual Screening Signup and view all the answers

What is the Latin expression for 'from the beginning' in the context of drug design?

De novo Signup and view all the answers

How does QSAR contribute to the lead optimization process in drug design?

By seeking the most active compounds of a series through minimizing expenses and manpower requirements Signup and view all the answers

What is pharmacophore modeling primarily used for in ligand based drug design?

To predict the biological activity or potency of new compounds Signup and view all the answers

What information can be used to design ligands specific to a target in De novo Drug Designing?

Active site composition and orientation of amino acids Signup and view all the answers

Which type of relationships does quantitative structure–activity relationship (QSAR) model represent?

Relationship between structural features and activity of query molecules Signup and view all the answers

Which method involves explicit molecular docking of ligands to the binding site of the target for scoring?

Structure Based Virtual Screening Signup and view all the answers

What is the main goal of the lead optimization process in drug design?

To systematically minimize expenses, delays, and manpower requirements Signup and view all the answers

What makes experimental testing easy and false positives tolerable in Structure Based Virtual Screening?

Availability of compounds in libraries Signup and view all the answers

Computational Tools for Protein Active Site Analysis and Ligand Design

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