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mmpd_lec1 - 20.181 Lecture 9 Contents 1 Placing atoms a la...

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20.181 Lecture 9 Contents 1 Placing atoms a la HW6 2 Protein design problem 3 Approach 4 What makes proteins fold? o 4.1 Entropy 5 Algorithm 6 Stunning Outdoor Interpretative bonding dance by TAs Placing atoms a la HW6 1. We can put the first atom (green) anywhere; put it at the origin 2. The second atom (blue) is placed a fixed distance away. It can be anywhere on the circle centered at the green dot, so we can choose to put it on the x-axis. 3. The third atom (red) defines the angle a123 and so it must be placed on the cone. But we also know it is a certain distance from the blue atom, so that constrains it to the "base" of the cone, the cirle perpendicular to the xy plane. We can choose to put it at the intersection with the xy plane. Protein design problem Given: protein backbone (a 3D structure) Find: amino acid sequence (1D) Build 3D protein structure incorporating known chemistry, rotation angles, torsion the chemistry of an amino acid is the same no matter what protein its in
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