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A structural and energetic description of protein-protein interactions in atomic detailFischer, Tiffany Brink 25 April 2007 (has links)
Here, we present the program QContacts, which implements Voronoi polyhedra
to determine atomic and residue contacts across the interface of a protein-protein
interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge
interactions, we focus on QContactsâ identification of atomic contacts in a protein
interface compared against the current methods. Initially, we investigated in detail the
differences between QContacts, radial cutoff and Change in Solvent Accessible Surface
Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface.
The results were assessed based on a set of 71 double cycle mutants. QContacts
excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and
the delta-SASA methods performed well at picking out direct contacts; however, QContacts
was the most accurate in excluding false positives. The significance of the differences
identified between QContacts and previous methods was assessed using pair-wise
contact frequencies in a broader set of 592 protein interfaces. The inaccuracies
introduced by commonly used radial cutoff methods were found to produce misleading
bias in the residue frequencies. This bias could compromise pair-wise potentials that are
based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available
methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons
(Fischer et al., 2006).
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Applications of Structural Bioinformatics for the Structural Genomics EraNovotny, Marian January 2007 (has links)
<p>Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation.</p><p>New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function. The functionality and performance of eleven fold-comparison servers were evaluated. None of the tested servers achieved perfect recall, so in practise a combination of servers should be used.</p><p>If fold comparison does not provide any hints about the function of a protein, structural motif searches can be employed. A survey of left-handed helices in known protein structures was carried out. The results show that left-handed helices are rare motifs, but most of them occur in active or ligand-binding sites. Their identification can therefore help to pinpoint potentially important residues.</p><p>Sometimes all available methods fail to provide hints about the function of a protein. Therefore, the potential of using docking techniques to predict which ligands are likely to bind to a particular protein has been investigated. Initial results show that it will be difficult to build a reliable automated docking protocol that will suit all proteins.</p><p>The effect of various phenomena on the precision of accessible surface area calculations was also investigated. The results suggest that it is prudent to report such values with a precision of 50 to 100 Å<sup>2</sup>.</p><p>Finally, a survey of register shifts in known protein structures was carried out. The identified potential register shifts were analysed and classified. A machine-learning approach ("rough sets") was used in an attempt to diagnose register errors in structures.</p>
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Applications of Structural Bioinformatics for the Structural Genomics EraNovotny, Marian January 2007 (has links)
Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation. New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function. The functionality and performance of eleven fold-comparison servers were evaluated. None of the tested servers achieved perfect recall, so in practise a combination of servers should be used. If fold comparison does not provide any hints about the function of a protein, structural motif searches can be employed. A survey of left-handed helices in known protein structures was carried out. The results show that left-handed helices are rare motifs, but most of them occur in active or ligand-binding sites. Their identification can therefore help to pinpoint potentially important residues. Sometimes all available methods fail to provide hints about the function of a protein. Therefore, the potential of using docking techniques to predict which ligands are likely to bind to a particular protein has been investigated. Initial results show that it will be difficult to build a reliable automated docking protocol that will suit all proteins. The effect of various phenomena on the precision of accessible surface area calculations was also investigated. The results suggest that it is prudent to report such values with a precision of 50 to 100 Å2. Finally, a survey of register shifts in known protein structures was carried out. The identified potential register shifts were analysed and classified. A machine-learning approach ("rough sets") was used in an attempt to diagnose register errors in structures.
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