<s>
Name	O
Data	O
License	O
Technology	O
Citations	O
Comments	O
Amira	B-Algorithm
EM	O
MM	O
MRI	O
Optical	O
SMI	O
XRD	O
Amira	B-Algorithm
commercial	O
license	O
Windows	B-Application
,	O
Linux	O
,	O
Mac	O
Based	O
on	O
OpenInventor/OpenGL	O
;	O
focusing	O
on	O
life	O
and	O
biomedical	O
sciences	O
.	O
</s>
<s>
Ascalaph	B-Application
Designer	I-Application
MM	O
MD	O
QM	O
C++	B-Language
Graphics	O
,	O
model	O
building	O
,	O
molecular	O
mechanics	O
,	O
quantum	O
chemistry	O
.	O
</s>
<s>
Avizo	B-Algorithm
EM	O
MM	O
MRI	O
Optical	O
SMI	O
XRD	O
Avizo	B-Algorithm
commercial	O
license	O
Windows	B-Application
,	O
Linux	O
,	O
Mac	O
Avizo	B-Algorithm
is	O
derived	O
from	O
Amira	B-Algorithm
and	O
focusing	O
on	O
materials	O
science	O
.	O
</s>
<s>
Avogadro	B-Language
MM	O
XRD	O
MD	O
open-source	O
,	O
GPL	O
C++	B-Language
,	O
Qt	B-Language
,	O
extensible	O
via	O
Python	B-Language
modules	O
BALL	O
Molecular	O
dynamics	O
MM	O
NMR	O
LGPL	B-Application
open-source	O
Standalone	B-General_Concept
program	I-General_Concept
Cn3D	B-Application
open-source	O
Standalone	O
programIn	O
the	O
NCBI	O
C++	B-Language
toolkit	O
Coot	B-Language
XRD	O
open-source	O
Gabedit	B-Language
XRD	O
MM	O
open-source	O
C	B-Language
Jmol	B-Language
open-source	O
Java	B-Device
applet	B-Language
or	O
standalone	B-General_Concept
program	I-General_Concept
Supports	O
advanced	O
capabilities	O
such	O
as	O
loading	O
multiple	O
molecules	O
with	O
independent	O
movement	O
,	O
surfaces	O
and	O
molecular	O
orbitals	O
,	O
cavity	O
visualization	O
,	O
crystal	O
symmetry	O
MDL	B-Application
Chime	I-Application
,	O
free	O
use	O
noncommercial	O
C++	B-Language
browser	B-Protocol
plugin	I-Protocol
for	O
Windows	B-Application
only	O
Build	O
and	O
visualize	O
molecule	O
and	O
periodic	O
systems	O
(	O
crystal	O
,	O
structures	O
,	O
fluids	O
...	O
)	O
,	O
animate	O
trajectories	O
,	O
visualize	O
molecular	O
orbitals	O
,	O
density	O
,	O
electrostatic	O
potential	O
...	O
visualize	O
graph	O
such	O
IR	O
,	O
NMR	O
,	O
dielectric	O
and	O
optical	O
tensors	O
.	O
</s>
<s>
Molden	B-Application
MM	O
XRD	O
,	O
free	O
use	O
academic	O
Molecular	B-Application
Operating	I-Application
Environment	I-Application
(	O
MOE	O
)	O
HM	O
MD	O
MM	O
NA	O
QM	O
SMI	O
XRD	O
Windows	B-Application
,	O
Linux	O
,	O
OS	O
X	O
;	O
SVL	O
programming	O
language	O
Build	O
,	O
edit	O
and	O
visualise	O
small	O
molecules	O
,	O
macromolecules	O
,	O
protein-ligand	O
complexes	O
,	O
crystal	O
lattices	O
,	O
molecular	O
and	O
property	O
surfaces	O
.	O
</s>
<s>
Molekel	B-Application
MM	O
XRD	O
open-source	O
Java	B-Language
3D	I-Language
applet	B-Language
or	O
standalone	B-General_Concept
program	I-General_Concept
PyMOL	B-Application
XRD	O
SMI	O
EM	O
Open-source	O
Python	B-Language
According	O
to	O
the	O
author	O
,	O
almost	O
1/4	O
of	O
all	O
published	O
images	O
of	O
3D	O
protein	O
structures	O
in	O
the	O
scientific	O
literature	O
were	O
made	O
via	O
PyMOL	B-Application
.	O
</s>
<s>
RasMol	B-Language
open-source	O
C	B-Language
standalone	B-General_Concept
program	I-General_Concept
SAMSON	B-Application
MM	O
MD	O
SMI	O
MRI	O
,	O
limited	O
free	O
version	O
Windows	B-Application
,	O
Linux	O
,	O
Mac	O
.	O
</s>
<s>
C++	B-Language
(	O
Qt	B-Language
)	O
SAMSON	B-Application
Connect	O
Computational	O
nanoscience	O
:	O
life	O
sciences	O
,	O
materials	O
,	O
etc	O
.	O
</s>
<s>
Modular	O
architecture	O
,	O
modules	O
termed	O
SAMSON	B-Application
Elements	O
.	O
</s>
<s>
Sirius	B-Application
open-source	O
Java	B-Language
3D	I-Language
applet	B-Language
or	O
standalone	B-General_Concept
program	I-General_Concept
No	O
longer	O
supported	O
as	O
of	O
2011	O
.	O
</s>
<s>
Scigress	B-Application
MM	O
QM	O
Scigress	B-Application
commercial	O
license	O
Standalone	B-General_Concept
program	I-General_Concept
Edit	O
,	O
visualize	O
and	O
run	O
simulations	O
on	O
various	O
molecular	O
systems	O
.	O
</s>
<s>
Spartan	B-Application
MM	O
QM	O
Spartan	B-Application
webpage	O
Standalone	O
programSpartan	O
Tutorial	O
&	O
User	O
's	O
Guide	O
Visualize	O
and	O
edit	O
biomolecules	O
,	O
extract	O
bound	O
ligands	O
from	O
PDB	O
files	O
for	O
further	O
computational	O
analysis	O
,	O
full	O
molecular	O
mechanics	O
and	O
quantum	O
chemical	O
calculations	O
package	O
with	O
streamlined	O
graphical	O
user	O
interface	O
.	O
</s>
<s>
UCSF	B-Application
Chimera	I-Application
XRD	O
SMI	O
EM	O
MD	O
open-source	O
for	O
noncommercial	O
useUCSF	O
Chimera	O
license	O
Python	B-Language
Includes	O
single/multiple	O
sequence	O
viewer	O
,	O
structure-based	O
sequence	O
alignment	O
,	O
automatic	O
sequence-structure	O
crosstalk	O
for	O
integrated	O
analyses	O
.	O
</s>
<s>
VMD	B-Application
EM	O
MD	O
MM	O
open-source	O
for	O
noncommercial	O
useVisual	O
Molecular	O
Dynamics	O
license	O
C++	B-Language
WHAT	B-Application
IF	I-Application
HM	O
XRD	O
,	O
shareware	B-License
for	O
academics	O
Fortran	B-Application
,	O
C	B-Language
,	O
OpenGL	B-Application
,	O
standalone	O
Old-fashioned	O
interface	O
;	O
very	O
good	O
software	O
for	O
the	O
experienced	O
bioinformatician	O
;	O
nearly	O
2000	O
protein-structure	O
related	O
options	O
;	O
comes	O
with	O
500	O
page	O
writeup	O
.	O
</s>
<s>
YASARA	B-Application
HM	O
NMR	O
XRC	O
,	O
limited	O
free	O
version	O
C-assembly	O
,	O
Windows	B-Application
,	O
Linux	O
,	O
Mac	O
Fully	O
featured	O
molecular	O
modeling	O
and	O
simulation	O
program	O
,	O
incl.	O
,	O
structure	O
prediction	O
and	O
docking	O
.	O
</s>
<s>
Graphical	O
or	O
text	O
mode	O
(	O
clusters	O
)	O
,	O
Python	B-Language
interface	O
.	O
</s>
