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location graph should have minima at locations that coincide with flexible hinges
between domains. We will explain these terms and methodology in detail.
We start with an energy minimization step, to relieve any close contacts or unnatural
bond lengths or angles in the undivided chain which would bias the results. For this we
use TINKER’s minimize routine with the OPLS-All Atom force field and the Ooi-
Scheraga Solvent Accessible Surface Area (SASA) continuum solvation free energy
term. For each iteration of the predictor, we introduce a cut between residues i - 1 and i.
This divides the protein into two fragments, numbered 1 and 2 (Figure 3.1). Fragment 1
is a polypeptide containing residues 1 to i - 1, and fragment 2 is another polypeptide
containing residues i to N, We use these fragments in an energetic calculation as follows.
We define E C as the single point energy of the complete (undivided) protein. This
includes bonded and non-bonded interactions. In the energy evaluation step we again use
the OPLS-All Atom force field with the SASA implicit solvent model. The energy
reported consists of two parts: the in vacuo potential energy of the molecule, and the free
energy of solvation, computed using the implicit solvent model, Note that this step will
change in the second variant of FlexOracle.
For each choice of cut location i, we compute fragment single point energies ( )
and E frag ( ) . We argue that ! E(i)
= ( )
2 i
E frag 1 i + 2 ( i)
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E frag 1 i
E frag - E C is related to the energy
change associated with hinge motion about the selected hinge, as follows.