<s>
FoldX	B-Application
is	O
a	O
protein	B-Application
design	I-Application
algorithm	O
that	O
uses	O
an	O
empirical	O
force	O
field	O
.	O
</s>
<s>
FoldX	B-Application
can	O
mutate	O
protein	O
and	O
DNA	O
side	O
chains	O
using	O
a	O
probability-based	O
rotamer	O
library	O
,	O
while	O
exploring	O
alternative	O
conformations	O
of	O
the	O
surrounding	O
side	O
chains	O
.	O
</s>
<s>
∆Smc	O
is	O
the	O
entropy	B-Algorithm
cost	O
for	O
fixing	O
the	O
backbone	O
in	O
the	O
folded	O
state	O
.	O
</s>
<s>
For	O
protein-protein	O
interactions	O
,	O
or	O
protein-DNA	O
interactions	O
FoldX	B-Application
calculates	O
∆∆G	O
of	O
interaction	O
:	O
</s>
<s>
∆Ssc	O
is	O
the	O
loss	O
of	O
translational	O
and	O
rotational	O
entropy	B-Algorithm
upon	O
making	O
the	O
complex	O
.	O
</s>
<s>
Native	O
FoldX	B-Application
is	O
run	O
from	O
the	O
command	B-Application
line	I-Application
.	O
</s>
<s>
A	O
FoldX	B-Application
plugin	O
for	O
the	O
YASARA	B-Application
molecular	O
graphics	O
program	O
has	O
been	O
developed	O
to	O
access	O
various	O
FoldX	B-Application
tools	O
inside	O
a	O
graphical	O
environment	O
.	O
</s>
<s>
in	O
silico	O
mutations	O
or	O
homology	O
modeling	O
with	O
FoldX	B-Application
can	O
be	O
directly	O
analyzed	O
on	O
screen	O
.	O
</s>
