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Theoretical studies of molecular rec...

Brooijmans, Natasja.

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Theoretical studies of molecular recognition.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Theoretical studies of molecular recognition./
Author:	Brooijmans, Natasja.
Description:	234 p.
Notes:	Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1740.
Contained By:	Dissertation Abstracts International64-04B.
Subject:	Chemistry, Pharmaceutical. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3088633

Theoretical studies of molecular recognition.
Brooijmans, Natasja.

Theoretical studies of molecular recognition. - 234 p.

Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1740.

Thesis (Ph.D.)--University of California, San Francisco, 2003.

Although numerous drugs currently in use were found serendipitously, more recently “rational” methods have been applied to drug discovery. This rational design has come from an understanding of how proteins and drugs interact, what the molecular bases of diseases are, and what the targets look like in three dimensions. Computational chemistry methods are indispensable in modern drug discovery. The use of computational chemistry tools can provide insight in the atomic basis for molecular recognition, and this information can guide the discovery and design of higher affinity, more specific drug molecules. In this dissertation I investigate the molecular recognition between proteins, and I assess the ability of the molecular docking program DOCK to capture molecular recognition.Subjects--Topical Terms:

550957
Chemistry, Pharmaceutical.

Theoretical studies of molecular recognition.
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035 $a (UnM)AAI3088633
035 $a AAI3088633
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100 1 $a Brooijmans, Natasja. $3 1947012
245 1 0 $a Theoretical studies of molecular recognition.
300 $a 234 p.
500 $a Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1740.
500 $a Adviser: Irwin D. Kuntz.
502 $a Thesis (Ph.D.)--University of California, San Francisco, 2003.
520 $a Although numerous drugs currently in use were found serendipitously, more recently “rational” methods have been applied to drug discovery. This rational design has come from an understanding of how proteins and drugs interact, what the molecular bases of diseases are, and what the targets look like in three dimensions. Computational chemistry methods are indispensable in modern drug discovery. The use of computational chemistry tools can provide insight in the atomic basis for molecular recognition, and this information can guide the discovery and design of higher affinity, more specific drug molecules. In this dissertation I investigate the molecular recognition between proteins, and I assess the ability of the molecular docking program DOCK to capture molecular recognition.
520 $a The importance of protein-protein interactions in humans has become clearer since the sequencing of the human genome. Many protein-protein interactions are important drug targets, but it has been difficult to disrupt these interactions with small molecules. In Chapter I, I analyze the relationship between complex stability and ligand size, and show that it is theoretically possible to design small molecules that have as high affinity for their protein receptor as protein ligands have.
520 $a I also showed in Chapter I that different biological classes of protein-protein complexes have different maximal stabilities. This led me to investigate in Chapter II which energy term makes certain protein-protein complexes more stable, which is shown to be the van der Waals interaction energy. This kind of information can be used in the design of small molecules to disrupt protein-protein complexes.
520 $a Docking programs are widely used in the pharmaceutical industry to find new leads or optimize existing leads for drug targets. Adequate testing is critically important in the development of docking algorithms. In Chapter III I compile a high-quality test platform and show its usefulness during algorithm development.
520 $a Chapter IV is a review of the computational chemistry field, and describes different tools, and their use. We also address the physical basis for molecular recognition and how different scoring functions try to capture the physics. Furthermore, we consider how different methods should be tested, as well as future applications.
590 $a School code: 0034.
650 4 $a Chemistry, Pharmaceutical. $3 550957
650 4 $a Health Sciences, Pharmacology. $3 1017717
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710 2 0 $a University of California, San Francisco. $3 1025118
773 0 $t Dissertation Abstracts International $g 64-04B.
790 1 0 $a Kuntz, Irwin D., $e advisor
790 $a 0034
791 $a Ph.D.
792 $a 2003
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3088633