<s>
Dong	O
,	O
Z	O
.	O
Peng	O
,	O
Y	O
.	O
Zhang	O
&	O
J	O
.	O
Yang2018	O
VAST	O
Vector	O
Alignment	O
Search	O
Tool	O
SSE	O
Pair	O
nil	O
server	O
S	O
.	O
Bryant	O
1996	O
PrISM	O
Protein	O
Informatics	O
Systems	O
for	O
Modeling	O
SSE	O
Multi	O
nil	O
server	O
B	O
.	O
Honig	O
2000	O
MOE	B-Application
Molecular	B-Application
Operating	I-Application
Environment	I-Application
.	O
</s>
<s>
Kleywegt	O
1997	O
SSM	O
Secondary	O
Structure	O
Matching	O
SSE	O
Multi	O
nil	O
server	O
E	O
.	O
Krissinel	O
2003	O
SHEBA	O
Structural	O
Homology	O
by	O
Environment-Based	O
Alignment	O
Seq	O
Pair	O
nil	O
server	O
J	O
Jung	O
&	O
B	O
Lee	O
2000	O
LGA	O
Local-Global	O
Alignment	O
,	O
and	O
Global	O
Distance	O
Test	O
(	O
GDT-TS	O
)	O
structure	O
similarity	O
measure	O
Cα	O
,	O
AllA	O
,	O
any	O
atom	O
Pair	O
nil	O
server	O
and	O
download	O
A	O
.	O
Zemla	O
2003	O
POSA	O
Partial	O
Order	O
Structure	O
Alignment	O
Cα	O
Multi	O
Yes	O
server	O
Y	O
.	O
Ye	O
&	O
A	O
.	O
Godzik	O
2005	O
PyMOL	B-Application
"	O
super	O
"	O
command	O
does	O
sequence-independent	O
3D	O
alignment	O
Protein	O
Hybrid	O
No	O
site	O
W	O
.	O
L	O
.	O
DeLano	O
2007	O
FATCAT	O
Flexible	O
Structure	O
AlignmenT	O
by	O
Chaining	O
Aligned	O
Fragment	O
Pairs	O
Allowing	O
Twists	O
Cα	O
Pair	O
Yes	O
server	O
Y	O
.	O
Ye	O
&	O
A	O
.	O
Godzik	O
2003	O
deconSTRUCT	O
Database	O
search	O
on	O
substructural	O
level	O
and	O
pairwise	O
alignment	O
.	O
</s>
<s>
2007	O
UCSF	B-Application
Chimera	I-Application
see	O
MatchMaker	O
tool	O
and	O
"	O
matchmaker	O
"	O
command	O
Seq	O
&	O
SSE	O
Multi	O
No	O
site	O
E	O
.	O
Meng	O
et	O
al	O
.	O
</s>
<s>
2008	O
Structal	O
Least	O
Squares	O
Root	O
Mean	O
Square	O
deviation	O
minimization	O
by	O
dynamic	O
programming	O
Cα	O
Pair	O
No	O
server	O
download	O
Gerstein	O
&	O
Levitt	O
2005	O
ProBiS	B-Protocol
Detection	O
of	O
Structurally	O
Similar	O
Protein	O
Binding	O
Sites	O
by	O
Local	O
Structural	O
Alignment	O
Surf	O
Pair	O
Yes	O
server	O
download	O
J	O
.	O
Konc	O
&	O
D	O
.	O
Janezic	O
2010	O
ALADYN	O
Dynamics-based	O
Alignment	O
:	O
superposing	O
proteins	O
by	O
matching	O
their	O
collective	O
movements	O
Cα	O
Pair	O
No	O
server	O
Potestio	O
et	O
al	O
.	O
</s>
<s>
2010	O
SWAPSC	B-Application
Sliding	O
Window	O
Analysis	O
Procedure	O
for	O
detecting	O
Selective	O
Constraints	O
for	O
analysing	O
genetic	O
data	O
structured	O
for	O
a	O
family	O
or	O
phylogenetic	O
tree	O
using	O
constraints	O
in	O
protein-coding	O
sequence	O
alignments	O
.	O
</s>
