lecture5 - Bioinformatics 2 lecture 5,6 Building a small...

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Bioinformatics 2 -- lecture 5,6 Building a small molecule Secondary structure prediction MOE Exercise 1
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Building aspartame
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Building aspartame Starting with an empty Moe window: •Edit-->Build-->Molecule (or Builder) •Create backbone using atoms buttons: N,C,C,N,C,C,O,C (Notice the chain is made in the fully reduced state.) •Add carbonyl oxygens: Select an H, hit O in Builder. the H becomes an O.
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Building aspartame •Select carbonyl groups. Click double bonds (=) • Add sidechains: •Select the front H on the second alpha-carbon. Click C, then benzene. •Select the back H on the first alpha-carbon. Click C, then - COO-
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Building aspartame Fix ionization of NH 3 Select N. In Builder, click "+1" (a proton is added) •Fix hybridization of NH. •Double-click second N. Choose Geometry: "sp2". Click "Apply" •Click "Minimize".
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What is energy minimization? Energy minimization is a molecular simulation the leads the system to a lower potential energy . This is similar to the problem of finding the parameters that minimize a function, but there are generally too many parameters. No optimal solution is possible. Energy minimization is a heuristic method.
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How is the energy of a molecular model calculated? Energy is a function of : (1) The coordinates of the atoms. (2) Their names . (3) Their numbers . The “names” and “numbers” tell the program what element the atoms are, how they are bonded , and what oxidation state they have.
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Molecular mechanics energy An energy function is a sum over a set of simple functions. This sum is the so-called “energy” of the system. E = f(a 1 ,a 2 ) + f(a 1 ,a 3 ) + f(a 2 ,a 3 ) + f(a 1 ,a 2 ,a 3 ) + etc. Each simple energy function (f) may have 2,3 or more atoms as parameters: coordinates, names and numbers. Each function uses stored information about each atom name to choose constants within each function. Together the entire set of functions and constants is called a “force field.”
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Molecular mechanics A molecular mechanics energy function includes the following components (and others): • bonded •bond lengths •bond angles •torsion angles •non-bonded •Lennard-Jones or Vander Waals •Coulomb, or electrostatic van der Waals spheres - + charge-charge interaction
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constraint/restraint restraint = a function that approaches a minimum as the parameters approach ideal values.
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lecture5 - Bioinformatics 2 lecture 5,6 Building a small...

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