Lecture 09
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Update Warning! This page has not been revised yet for the 2007 Fall term. Some of the slides may be reused, but please consider the page as a whole out of date as long as this warning appears here.
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Structure Analysis
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Lecture Slides
Slide 001
Lecture 09, Slide 001
Slide 002
Lecture 09, Slide 002
Slide 003
Lecture 09, Slide 003
Slide 004
Lecture 09, Slide 004
Slide 005
Lecture 09, Slide 005
Rotamers are low-energy conformations of side-chain dihedral angles. Only a small number of rotamer states and combinations are significantly populated in natural proteins. This tremendously simplifies protein structure modelling and prediction problems. However it also guides analysis, e.g. in enzyme active sites the rotamers often exist in strained, rare conformations.
Rotamers are low-energy conformations of side-chain dihedral angles. Only a small number of rotamer states and combinations are significantly populated in natural proteins. This tremendously simplifies protein structure modelling and prediction problems. However it also guides analysis, e.g. in enzyme active sites the rotamers often exist in strained, rare conformations.
Slide 006
Lecture 09, Slide 006
Surfaces represent the parts of a protein that interact with the surroundings. In this example, the electrostatic potential mapping shows how an electrostatic potential gradient attracts the substrate molecule into Acetylcholine-esterase's active site.
Surfaces represent the parts of a protein that interact with the surroundings. In this example, the electrostatic potential mapping shows how an electrostatic potential gradient attracts the substrate molecule into Acetylcholine-esterase's active site.
Slide 007
Lecture 09, Slide 007
The "Accessible Surface" depends on the probe radius. For solvent accessible surfaces a probe radius of 1.4A is commonly used since this approximates the radius of a water-molecule.
The "Accessible Surface" depends on the probe radius. For solvent accessible surfaces a probe radius of 1.4A is commonly used since this approximates the radius of a water-molecule.
Slide 008
Lecture 09, Slide 008
Motifs represent (presumably) low-energy patterns of conformations. They can be discovered in structure datasets by looking for patterns that recur more frequently than expected by random chance. In almost all cases, they have significant statistical propensities to favour particular amino acids in particular positions.
Motifs represent (presumably) low-energy patterns of conformations. They can be discovered in structure datasets by looking for patterns that recur more frequently than expected by random chance. In almost all cases, they have significant statistical propensities to favour particular amino acids in particular positions.
