BMD409: Structural Bioinformatics Lecture 5 - Protein Structure Modeling

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What is the primary goal of protein threading in structure modeling?

To identify the fold of proteins with unknown structures (correct)

To model proteins with known structures

To determine the sequence of proteins with known folds

To predict the structure of proteins without known structures

What is the difference between ab initio modeling and template-based modeling?

Ab initio modeling does not use known structures, while template-based modeling does (correct)

Ab initio modeling uses known structures, while template-based modeling does not

Ab initio modeling is used for protein sequencing, while template-based modeling is for protein structure prediction

Ab initio modeling is used for protein structure prediction, while template-based modeling is for protein sequencing

What is the term used to describe the collection of proteins used in protein threading?

Sequence archive

Protein repository

Fold library (correct)

Structure database

What is the purpose of the 'goodness of fit' score in protein threading?

To evaluate the alignment of the target sequence with the template structures Signup and view all the answers

Which of the following methods is used when there is no available structure for a protein?

Ab initio modeling Signup and view all the answers

What is the basis of the 'goodness of fit' score in protein threading?

Empirical energy function based on statistics derived from known protein structures Signup and view all the answers

What is a crucial aspect of successful ab initio modeling?

An efficient search method Signup and view all the answers

What is the primary purpose of ab initio modeling?

To understand the folding process of proteins Signup and view all the answers

What type of scoring function is particularly useful in protein threading?

Scoring function with pairwise and solvation terms Signup and view all the answers

What is the main difference between fragment-based and biophysics-based ab initio modeling methods?

The type of energy function used Signup and view all the answers

What is the advantage of using ab initio modeling over template-based modeling?

Ab initio modeling can be used for proteins with no known homologs Signup and view all the answers

What is the role of molecular mechanics and quantum mechanics in protein engineering?

To improve the accuracy of scoring functions Signup and view all the answers

What is the primary goal of ab initio modeling approaches in protein structure prediction?

To build protein structures from small structural pieces Signup and view all the answers

What is the process of finding the conformation of a protein that minimizes its total energy?

Energy minimization Signup and view all the answers

What is the purpose of gathering a collection of known protein structures in protein threading?

To serve as templates for modeling Signup and view all the answers

What is the primary difference between ab initio modeling and template-based modeling?

The use of homologous structures or templates Signup and view all the answers

What is the purpose of choosing the best-fitting template in template-based modeling?

To construct a model of the target protein based on the alignment Signup and view all the answers

What is the goal of protein threading?

To model proteins by aligning their sequences with known protein folds and calculating a goodness-of-fit score Signup and view all the answers