Molecular Modelling Softwares-Open Sources available for Drug Design & Discovery

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2 Δεκ 2013 (πριν από 3 χρόνια και 11 μήνες)

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Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

12

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Molecular Modelling Softwares
-
Open
Sources available for Drug Design &
Discovery


P. N. Kishore Babu
*, Ashok Kumar Taduri
¥



*
Department of Chemistry, JNTUH College of Engineering, Kukatpally,
Hyderabad (A.P), India
-
500 085.

Email:
kishore1136@gmail.com




What is Molecular Modelling?


Molecular modeling

encompasses all theoretical methods and computational
tech
niques used to

model

or mimic the behaviour of

molecules
. The techniques
are used in the fields of

computational chemistry
,
drug design
,

computational
biology

and

materials science

for studying molecular systems ranging from
small chemical systems to large biological molecules and material assemblies.
The simplest calculations can be performed by hand, but inevitably computers
are required to p
erform molecular modelling of any reasonably sized system.
The common feature of molecular modelling techniques is the atomistic level
description of the molecular systems. This may include treating atoms as the
smallest individual unit (the
Molecular mechanics

approach), or explicitly
modeling electrons of each atom (the

quantum chemistry
approach).



List of Free Softwares availabl
e


This is a list of computer programs that are predominantly used for

molecular
mechanics

calculations.


Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

13

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.



Min
-

Optimiz
ation
, MD
-

Molecular Dynamics
, MC
-

Monte Carlo
, REM
-

Replica exchange

method,
QM
-
Quantum mechanics
, Imp
-

Implicit water, HA
-

Hardware accelerated
.


Y
-

Yes.


I
-

Has int
erface.




Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
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p

G
P
U

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Licens
e

Website

Abalone

Y

Y

Y

Y

Y

Y

I

Y

Y

Biomolecular
simulations, prote
in
folding.

Free

Agile Molecule

ACEMD
[
1]



Y

Y





Y

Molecular dynamics
with CHARMM,
Amber forcefields.
Running on NVIDIA
GPUs. Heavily
optimized with
CUDA.

Basic
version
free.
Commerci
al version
available.

Acellera Ltd

ADUN
[2]



Y

Y



Y

Y

Y

Charmm, AMBER,
user specified
(through force field
markup language,
FFML), QM/MM
calculations with
Empirical Valence
Bond (EVB);
Framework based
(GNUStep/cocoa);
SCAAS for spherical
boundary conditions

Free

adun.imim.es

AMBER
[
3]


Y

Y

Y


Y


Y

Y


N
ot free

ambermd.org

Ascalap
h
Designe
r

Y

Y

Y

Y

Y

Y

I

Y

Y

Molecular building
(DNA, proteins,
hydrocarbons,
nanotubes).

Molecular dynami
cs.
GPU acceleration.

Free &
Commerci
al

Ascalaph Project

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

14

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

Automa
ted
Topolog
y
Builder
(ATB)


Y

Y







Automated
molecular topology
building service for
small molecules (<
99 atoms).
GROMOS,
GROMACS, CNS
formats with
validation

Repository for
molecular topologies
and pre
-
e
quilibrated
systems

Free for
academic
use

Automated
Topology Builder

Avogadr
o

Y

Y

Y




I



Molecule building,
edi
ting (Peptides,
small molecules,
crystals),
Conformational
analysis, 2D/3D
conversion.
Extensible interfaces
to other tools.

Free,
open
source

Avogadro

Balloon


Y

Y







2D/3D conversion
and conformational
analysis.

Free to
use,
closed
source

Åbo Akademi

BOSS



Y


Y


Y



OPLS

Commerci
al

Yale University

CHARM
M


Y

Y

Y

Y

I

I

Y


Commercial version
with multiple
graphical front ends
is sold
by

Accelrys

(as
CHARMm)

Not free

charmm.org

Chemito
rium

Y

Y








Free 2D/3D

graphical organic
molecule builder,
viewer and
visualisation tool.

Free

link

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

15

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

ChemS
ketch

Y

Y

Y







Fast 2
-
D graphical
molecule builder
and 3
-
D viewer.
Contains simplified
CHARMM for fast
stable inaccurate
optimization of
single molecules up
to 1000 atoms

Free

Advanced
Chemistry
Development, Inc.

COSMO
S

Y

Y

Y

Y

Y


I



Hybrid QM/MM
COSMOS
-
NMR force
field with fast semi
-
empirical calculation
of electrostatic
and/or NMR
properties. 3
-
D
graphical molecule
builder and viewer.

Free
(without
GUI) and
commerci
al

COSMOS Software

Culgi

Y

Y

Y

Y

Y





Atomistic
simulations and
mesoscale methods.

Not free

Culgi BV

Deneb

Y

Y

I

I



I



Deneb is a powerful
application capable
of managing
hundreds of
projects, each
containing hundreds
of simulations
applied to different
samples,every one
containing
thousands of atoms.

Deneb interfaces
with mos
t relevant
simulation packages
(SIESTA, QE,
VASP,etc.): Launch
your simulation into
Commerci
al/Trial
available

AtelGrap
hics inc.

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

16

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
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Comments

Licens
e

Website

a remote host with a
single click, Deneb
will monitor them for
you and retrieve the
outputs.

Desmon
d

Y

Y

Y

Y


Y



Y

High Performance
MD. Comes with a
comprehensive GUI
for building,
visualizing, and
reviewing results as
well as calculation
setup up
and
launching.

Free and
commerci
al

D. E. Shaw
Research
Schrödin
ger

Discove
ry
Studio

Y

Y

Y

Y

Y


Y

Y


Discovery Studio is a
comprehensive life
science modeling
and simulation suite
of applications
focused on
optimizing the drug
discovery process.
Capabilities include,
small molecule
simulations,
QM/MM,
pharmaco
phore
modeling, QSAR,
protein
-
ligand
docking, protein
homology modeling,
sequence analysis,
protein
-
protein
docking, antibody
modeling, etc.

Closed
source/Tr
ial
available

Accelrys

fold.it

Y / I

Y

Y

Y

Y

Y

I



University of
Washington and The
Baker Labs.
Free,
download

fold.it download
page

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

17

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

Structure prediction.
Protein folding.

FoldX

I

Y

Y







Energy calculations
and protein design

Free for
academic
use

CRG

GoVASP

Y


I

I



I



GoVASP is a
sophisticated
graphical user
interface for the
Vienna Ab
-
Initio
Simulation Package
(VASP). GoVASP
comprises tools to
prepare, perform
and monitor VASP
calculations and to
evaluate and
visuali
ze the
computed data.

Closed
source/N
ot
free/Trial
available

Windiks
Consulting

GPIUTM
D

I

I

Y

Y


I



Y

GPIUTMD stands for
Graphic Processors
at
Isfahan University
of Technology

for
Many
-
particle
Dynamics. It
performs general
purpose p
article
dynamics
simulations on a
single workstation,
taking the advantage
of NVIDIA CUDA
GPUs to attain a
level of performance
equivalent to
hundreds of
processors on a fast
cluster.

Closed
source/N
ot
free/Dem
o
available

GPIUTMD

GROMA
CS




Y


Y



Y

High performance
MD

Free

gromacs.org

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

18

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

GRO
MO
S



Y

Y

Y

Y


Y

Y

Geared towards
biomolecules

Not free

GROMOS
Homepage

GULP



Y

Y






Molecular dynamics
and Lattice
optimization

Free for
academic
use

https://projec
ts.iv
ec.org/gulp/

HOOMD
-
blue



Y

Y





Y

General
-
purpose
Molecular Dynamics
highly optimized for
GPUs. Includes
various pair
potentials, Brownian
dynamics,
dissipative particle
dynamics, rigid body
constraints, energy
minimization, etc...

Free,
open
sour
ce

http://codeblue.u
mich.edu/hoomd
-
blue/index.html

ICM

Y

Y

Y


Y


I

Y


Powerful global
optimizer in an
arbitrary subset of
internal variables,
NOEs, Protein
docking, Ligand
docking, Peptide
do
cking, EM,
Density placement

Not free

Molsoft

LAMMP
S



Y

Y

Y

Y

I


Y

Has potentials for
soft and solid
-
state
materials and
coarse
-
grain
systems

Free

Sandia

MacroM
odel

Y

Y

Y

Y

Y


I

Y


OPLS
-
AA, MMFF,
GBSA solvent model,
conformational
sampling,
minimization, MD.
Includes the Maestro
GUI which p
rovides
visualization,
molecule building,
Commerci
al

Schr
ödinger

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

19

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

calculation setup,
job launching and
monitoring, project
-
level organization of
results and access to
a suite of other
modelling programs.

MAPS

Y

Y

Y

Y

Y


Y


Y

Building,
visualization and
analysis tools in a
single user interf
ace
together with access
to multiple
simulation engines.

Closed
source/Tr
ial
available

Scienomics

Material
s Studio

Y

Y

Y

Y

Y


Y

Y

Y

Materials Studio is a
software
environment that
brings the materials
simulation
technology to
desktop computing,
solving key problems
throughout the R&D
process.

Closed
source/Tr
ial
available

Accelrys

MedeA

Y

Y

Y

Y

Y


Y



MedeA combines
leading experimental
databases and major
computatio
nal
programs like the
Vienna Ab
-
Initio
Simulation Package
(VASP), LAMMPS,
GIBBS with
sophisticated
materials property
prediction, analysis,
and visualization.

Closed
source/Tr
ial
available

Materials Design

MCCCS
Towhee





Y





Originally designed
for the prediction of
fluid phase
Free

Towhee Project

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

20

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
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Comments

Licens
e

Website

equilibria

MDyna
Mix




Y






Parallel MD

Free

Stockholm
University

MOE

Y

Y

Y

Y



I

Y


Molecular Operating
Environment

Commerci
al

Chemical
Computing Group

MOIL

Y

Y

Y

Y






Also includes action
-
based algorithms
(Stochastic
Difference Equation
in Time and
Stochastic
Difference Equation
in Length) and
locally enhanced
sampling.

Free

link

molecoo
ls

Y

Y








Simple Javascript
molecular
vi
sualization tool


link

MOLDY




Y






Parallel, only pair
-
potentials,

Cell lists
,
modified

Beeman's
algorithm

Free

Moldy

ORAC



Y

Y


Y


Y


A Molecular
Dynamics
Simulation Program
to Explore Free
Energy Surfaces in
Biomolecular
Systems at the
Atomistic Level

Free,
open
source

ORAC download
page

NAB
[4]


Y








Generation of
Models for
"Unusual" DNA and
RNA

Free

Case group

Packmo
l


Y








Builds complex
initial configurations
for Molecular
Dynamics


link

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

21

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
U

Comments

Licens
e

Website

Prime

Y

Y

Y


Y


I

Y


Homology modeling,
loop and side chain
optimization,
minimization, OPLS
-
AA, SGB solvent
model, parallalized

Commerci
al

Schrödinger

Protein
Local
Optimiz
ation
Program


Y

Y

Y

Y





Helix, loop, and side
chain optimizati
on.
Fast energy
minimization.

Not free

PLOP wiki

p4vasp

Y

Y








Python
-
based
viewer, structure
builder and VASP
results browser.
Shows band
-
structure, charge
densities and
simulates STM
images.

Free,
open
source

p4vasp.at

PyMOL

Y

Y








Python
-
based
viewer, ma
ny
plugins to other
software. Some
mutagenisis.

Free,
open
source

PyMol.org

QMOL

Y









Protein v
iewer,
provided
by

DNASTAR

Free

DNASTAR, Inc.

RasMol

Y









Fast viewer

Free

RasMol

Raster3
D

Y









High quality rast
er
images

Free

University of
Washington

RedMD
[
5]

I

Y

Y

Y

Y





Reduced MD.
Package for coarse
-
grained simulations.

Free on
GNU
Licence

University of
War
saw, ICM

StruMM
3D
(STR3DI
32)

Y

Y

Y

Y

'


'



Sophisticated 3
-
D
molecule builder
and viewer,
advanced structu
ral
The 200
atom
version is
free

Exorga, Inc.

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

22

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

View

3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
P
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Comments

Licens
e

Website

analytical
algorithms, full
featured molecular
modeling and
quantitation of
stereo
-
electronic
effects, docking and
the handling of
complexes.

Selvita
Protein
Modelin
g
Platfor
m

Y

Y

Y


Y





Protein structure
prediction
,

homology
modeling
,

ab
initio

modeling,

loop
modeling
,
protein
threading

Commerci
al

Selvita Ltd

SCIGRE
SS

Y

Y

Y

Y



Y

Y


MM
,

DFT
,

Semiempi
rical methods
,
parallel
MD
,
conformational
analysis, Linear
scaling SCF,

docking
protein
-
ligand
,

Batch
processing
,

Virtual
screening
,
Automated builders
(molecular
dynamics, proteins,
crystals)

Commerci
al

SCIGRESS.com

SimBio
Sys'
MoDeST
(Molecul
ar
Design
Sof
twar
e
Toolkit)

Y

Y

Y






Y

molecular
docking
,

scoring
funct
ions for
docking
, "ligand
-
based", "fragment
-
based", "de
-
novo"

Not Free

SimBioSys Inc.

Spartan

Y

Y

Y


Y


Y

Y


Small molecule (<
2000 a.m.u.) MM
Commerci
al, Trial
Wavefunction, Inc.

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

23

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

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el

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der

Min

MD

M
C

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Website

and QM tools for
determining
conformation,
structure, property,
spectra, reactivity,
and selectivity.

Available

SwissPa
ram










Web server to
determine
automatically
parameters and
topologies for small
organic molecules,
for use with the
CHARM
M all atoms
force field. Files can
be used with
CHARMM and
GROMACS.

Free for
academic.
CHARMm
licence
required
for
commerci
al usage.

SwissParam.

T
eraChe
m



Y

Y



Y


Y

High
performance

GPU
-
accelerated

ab
initio
Molecular
Dynamics

and
TD/
DFT

software
package for very
large

molecular

or
even
nanoscale

s
yste
ms. The software
runs
on
NVIDIA

GPUs

and

64
-
bit

Linux
, and is
based on heavily
optimized

CUDA

cod
e.

Closed
source /
Trial
licenses
available

PetaChem LLC

TINKER

I

Y

Y

Y

Y


I

Y


Software tools for
molecular design

Free

Washington
University

Tremolo
-
X

I


Y

Y






Fast, parallel MD

Not Free

Tremolo
-
X

UCSF
Y

Y

Y







Visually appealing

University of
Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

24

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

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3D

Mod
el

Buil
der

Min

MD

M
C

RE
M

Q
M

I
m
p

G
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e

Website

Chimer
a

viewer, amino acid
rotamers
and other
building, includes
Antechamber and
MMTK, Ambertools
plugins in
development.

California

VEGA
ZZ

Y

Y

Y

I

Y



Y

Y

3D viewer, multiple
file format support,
2D and 3D editor,
surface calculation,
conformational
analysis,

MOPAC

an
d

NAMD
interfaces,
MD trajectory
analysis, molecular
docking, virtual
screening, database
engine, parallel
design,

OpenCL

acce
leration, etc.

Free for
a
cademic
use

VEGA ZZ Web site

VLifeM
DS

Y

Y

Y


Y


I


Y

Complete Molecular
Modelling Software,

QSAR,
Combinetorial
Library generation,
Pharmacophore,
Cheminformatics,
docking, etc.

Not free

Vlife Sciences
Technologies

VMD

+

NAMD

Y

Y

Y

Y


Y


Y

Y

Fast, parallel MD,
CUDA

Open
source,
free to
academic
s

Beckman Institute

WHAT
IF

Y

Y

I

I

I





Visualizer for MD.
Interface to
GROMACS.

Not free

WHAT IF

xeo

Y

Y








open project
management for

link

Open Access Chemistry
-
The Blog Journal

Vol 1, Issue1, 13
-
26, 2013. Visit: www.openaccess
-
chemistry.com

25

Blog Journal: A journal which focus on short and st
raight articles which publishes the articles in
respective field or area, also presented online by blogging.


Nam
e

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el

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der

Min

MD

M
C

RE
M

Q
M

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p

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e

Website

nanostructures

YASARA

Y

Y

Y

Y



Y



Molecular
-
graphics,
-
modeling and
-
simulation program

Not free

YASARA.org

Zodiac

Y

Y

Y







Drug design suite


link



If you are a beginner in Molecular Modelling then here a book is for You to
download free (OPEN access).


References


Molecular Modelling for Beginners, Second Edition

Publisher:JohnWiley & Sons Ltd 2008 | 411 Pages | ISBN: 9780470513132.


1.
http://depositfiles.com/files/fmpvfsoip



2.
http://www.mediafire.com/download/o13ar3946b43v86/9780470513132.rar