Editing Protein design (section)

====Challenges for effective design energy functions====
Water makes up most of the molecules surrounding proteins and is the main driver of protein structure. Thus, modeling the interaction between water and protein is vital in protein design. The number of water molecules that interact with a protein at any given time is huge and each one has a large number of degrees of freedom and interaction partners. Instead, protein design programs model most of such water molecules as a continuum, modeling both the hydrophobic effect and solvation polarization.<ref name="boas2007" />

Individual water molecules can sometimes have a crucial structural role in the core of proteins, and in protein–protein or protein–ligand interactions. Failing to model such waters can result in mispredictions of the optimal sequence of a protein–protein interface. As an alternative, water molecules can be added to rotamers.
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====Lennard-Jones potentials====

====Electrostatics====

====Entropy====

To be done.

====Non-pairwise terms====

Polarizability ... to be done.

====Knowledge-based energy functions====
--><ref name="boas2007" />

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====Lennard-Jones potentials====

====Electrostatics====

====Entropy====

To be done.

====Non-pairwise terms====

Polarizability ... to be done.

====Knowledge-based energy functions====
-->