<s>
ProBiS	B-Protocol
is	O
a	O
computer	O
software	O
which	O
allows	O
prediction	O
of	O
binding	O
sites	O
and	O
their	O
corresponding	O
ligands	O
for	O
a	O
given	O
protein	O
structure	O
.	O
</s>
<s>
Initially	O
ProBiS	B-Protocol
was	O
developed	O
as	O
a	O
ProBiS	B-Protocol
algorithm	O
by	O
Janez	O
Konc	O
and	O
Dušanka	O
Janežič	O
in	O
2010	O
and	O
is	O
now	O
available	O
as	O
ProBiS	B-Protocol
server	O
,	O
ProBiS	B-Protocol
CHARMMing	O
server	O
,	O
ProBiS	B-Protocol
algorithm	O
and	O
ProBiS	B-Protocol
plugin	B-Application
.	O
</s>
<s>
The	O
name	O
ProBiS	B-Protocol
originates	O
from	O
the	O
purpose	O
of	O
the	O
software	O
itself	O
,	O
that	O
is	O
to	O
predict	O
for	O
a	O
given	O
Protein	O
structure	O
Binding	O
Sites	O
and	O
their	O
corresponding	O
ligands	O
.	O
</s>
<s>
ProBiS	B-Protocol
software	O
started	O
as	O
ProBiS	B-Protocol
algorithm	O
that	O
detects	O
structurally	O
similar	O
sites	O
on	O
protein	O
surfaces	O
by	O
local	O
surface	O
structure	O
alignment	O
using	O
a	O
fast	B-Algorithm
maximum	I-Algorithm
clique	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
The	O
ProBiS	B-Protocol
algorithm	O
was	O
followed	O
by	O
ProBiS	B-Protocol
server	O
which	O
provides	O
access	O
to	O
the	O
program	O
ProBiS	B-Protocol
that	O
detects	O
protein	O
binding	O
sites	O
based	O
on	O
local	O
structural	O
alignments	O
.	O
</s>
<s>
There	O
are	O
two	O
ProBiS	B-Protocol
servers	O
available	O
,	O
ProBiS	B-Protocol
server	O
and	O
ProBiS	B-Protocol
CHARMMing	O
server	O
.	O
</s>
<s>
The	O
latter	O
connects	O
ProBiS	B-Protocol
and	O
CHARMMing	O
servers	O
into	O
one	O
functional	O
unit	O
that	O
enables	O
prediction	O
of	O
protein−ligand	O
complexes	O
and	O
allows	O
for	O
their	O
geometry	O
optimization	O
and	O
interaction	O
energy	O
calculation	O
.	O
</s>
<s>
The	O
ProBiS	B-Protocol
CHARMMing	O
server	O
with	O
these	O
additional	O
functions	O
can	O
only	O
be	O
used	O
at	O
National	O
Institutes	O
of	O
Health	O
,	O
USA	O
.	O
</s>
<s>
Otherwise	O
it	O
acts	O
as	O
a	O
regular	O
ProBiS	B-Protocol
server	O
.	O
</s>
<s>
Additionally	O
a	O
ProBiS	B-Protocol
PyMOL	B-Application
plugin	B-Application
and	O
ProBiS	B-Protocol
UCSF	B-Application
Chimera	I-Application
plugin	B-Application
have	O
been	O
made	O
.	O
</s>
<s>
Both	O
plugins	B-Application
are	O
connected	O
via	O
the	O
internet	O
to	O
a	O
newly	O
prepared	O
database	O
of	O
pre-calculated	O
binding	O
site	O
comparisons	O
to	O
allow	O
fast	O
prediction	O
of	O
binding	O
sites	O
in	O
existing	O
proteins	O
from	O
the	O
Protein	O
Data	O
Bank	O
.	O
</s>
<s>
The	O
ProBiS	B-Protocol
algorithm	O
structurally	O
compares	O
the	O
query	O
independently	O
of	O
sequence	O
or	O
fold	O
with	O
a	O
database	O
of	O
non-redundant	O
protein	O
structures	O
.	O
</s>
<s>
The	O
ProBiS	B-Protocol
algorithm	O
compares	O
structures	O
based	O
on	O
geometry	O
as	O
well	O
as	O
physicochemical	O
properties	O
and	O
returns	O
their	O
local	O
structural	O
alignment	O
.	O
</s>
<s>
ProBiS	B-Protocol
web	B-Application
server	I-Application
RESTful	O
Web	O
ServicesThe	O
ProBiS	B-Protocol
web	B-Application
server	I-Application
features	O
RESTful	O
(	O
Representational	O
State	O
Transfer	O
)	O
web	O
services	O
to	O
make	O
the	O
binding	O
site	O
similarities	O
and	O
local	O
pairwise	O
alignments	O
for	O
any	O
PDB	O
protein	O
structure	O
easily	O
accessible	O
from	O
any	O
script	O
.	O
</s>
<s>
ProBiS-Database	O
accessProBiS-Database	O
can	O
be	O
accessed	O
directly	O
from	O
ProBiS	B-Protocol
(	O
CHARMMing	O
)	O
server	O
,	O
ProBiS-Database	O
widget	O
,	O
which	O
can	O
be	O
included	O
in	O
any	O
web	O
page	O
to	O
provide	O
access	O
to	O
the	O
ProBiS-Database	O
,	O
or	O
RESTful	O
Web	O
Services	O
,	O
which	O
make	O
ProBiS-Database	O
easily	O
accessible	O
from	O
any	O
script	O
.	O
</s>
