FPGA Computing in Modern Bioinformatics - Parallel Computing for Bioinformatics and Computational Biology - page 724

Interaction
energy

E Penalty

Simple energy function 1

Maximum Maximum ABS

Minimum

Function 1

E 0

Interaction
energy

E Penalty

Precise energy function 2

Maximum ABS

Minimum Maximum

Function 2

E 0 values

Figure 28.7 Used energy function for the contact pair potentials. The upper diagram shows
the applied simple energy function 1 and the lower diagram shows the more precise energy
function 2.

into account and checks if the evaluated atoms are from the same amino acid, from
a neighboring amino acid or from a non-neighboring amino acid. Atom pair interac-
tions from atoms that are located within the same amino acid do not contribute an
energy term to the total energy. These energy values are set to zero. Atom pairs from
neighboring amino acids are evaluated using a different interaction value table as it
is used for atom pairs which are from non-neighbor amino acids.

28.5.3 Energy Calculation Algorithm

The total energy of a protein in this model is the sum of the contact energies between
all atom pairs. Therefore, the algorithm for calculating the total energy must loop over
all atom pairs and calculate the individual distance between the two selected atoms.