Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com 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: [email protected]
What is Molecular Modelling?
Molecular modeling encompasses all theoretical methods and computational techniques 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 perform 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 (theMolecular mechanics approach), or explicitly modeling electrons of each atom (the quantum chemistryapproach).
List of Free Softwares available
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
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Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, REM - Replica exchange method, QM -Quantum mechanics, Imp - Implicit water, HA - Hardware accelerated.
Y - Yes.
I - Has interface.
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
Biomolecular
Abalone Y Y Y Y Y Y I Y Y simulations, protein Free Agile Molecule folding.
Molecular dynamics Basic with CHARMM, version Amber forcefields. ACEMD[ free.
Y Y Y Running on NVIDIA Acellera Ltd 1] Commerci GPUs. Heavily al version optimized with available. CUDA.
Charmm, AMBER, user specified (through force field markup language, FFML), QM/MM calculations with [2] ADUN Y Y Y Y Y Free adun.imim.es Empirical Valence Bond (EVB); Framework based (GNUStep/cocoa); SCAAS for spherical boundary conditions
AMBER[
Y Y Y Y Y Y Not free ambermd.org 3]
Molecular building Ascalap (DNA, proteins, Free & h hydrocarbons,
Y Y Y Y Y Y I Y Y Commerci Ascalaph Project Designe nanotubes). al r Molecular dynamics. GPU acceleration.
13 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
Automated molecular topology building service for small molecules (< Automa 99 atoms). ted GROMOS, Free for Topolog Automated Y Y GROMACS, CNS academic y Topology Builder formats with use Builder validation
(ATB) Repository for molecular topologies and pre-equilibrated systems
Molecule building, editing (Peptides, small molecules, crystals), Free, Avogadr
Y Y Y I Conformational open Avogadro o analysis, 2D/3D source conversion. Extensible interfaces to other tools.
Free to 2D/3D conversion use,
Balloon Y Y and conformational Åbo Akademi closed analysis. source
Commerci
BOSS Y Y Y OPLS Yale University al
Commercial version with multiple CHARM graphical front ends
Y Y Y Y I I Y Not free charmm.org
M is sold by Accelrys (as CHARMm)
Free 2D/3D graphical organic Chemito
Y Y molecule builder, Free link rium viewer and visualisation tool.
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Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified Advanced ChemS Y Y Y CHARMM for fast Free Chemistry ketch
stable inaccurate Development, Inc. optimization of single molecules up to 1000 atoms
Hybrid QM/MM COSMOS-NMR force field with fast semi- Free empirical calculation (without COSMO
Y Y Y Y Y I of electrostatic GUI) and COSMOS Software
S and/or NMR commerci properties. 3-D al graphical molecule builder and viewer.
Atomistic
Culgi Y Y Y Y Y simulations and Not free Culgi BV
mesoscale methods.
Deneb is a powerful application capable of managing hundreds of projects, each containing hundreds of simulations applied to different
samples,every one Commerci containing Deneb Y Y I I I al/Trial AtelGraphics inc.
thousands of atoms. available
Deneb interfaces
with most relevant
simulation packages
(SIESTA, QE,
VASP,etc.): Launch
your simulation into 15 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
a remote host with a
single click, Deneb
will monitor them for
you and retrieve the
outputs.
High Performance MD. Comes with a comprehensive GUI for building, Free and D. E. Shaw Desmon Y Y Y Y Y Y visualizing, and commerci ResearchSchrödin d
reviewing results as al ger well as calculation setup up and launching.
Discovery Studio is a comprehensive life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Capabilities include, Closed Discove small molecule source/Tr ry Y Y Y Y Y Y Y simulations, Accelrys ial
Studio QM/MM, available pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc.
University of Free, fold.it download fold.it Y / I Y Y Y Y Y I Washington and The
download page Baker Labs. 16 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
Structure prediction. Protein folding.
Free for Energy calculations
FoldX I Y Y academic CRG and protein design use
GoVASP is a sophisticated graphical user interface for the Vienna Ab-Initio Closed Simulation Package source/N (VASP). GoVASP Windiks
GoVASP Y I I I ot
comprises tools to Consulting free/Trial prepare, perform available and monitor VASP calculations and to evaluate and visualize the computed data.
GPIUTMD stands for Graphic Processors atIsfahan University of Technology for Many-particle Dynamics. It performs general Closed purpose particle source/N dynamics GPIUTM ot
I I Y Y I Y simulations on a GPIUTMD
D free/Dem single workstation, o taking the advantage available of NVIDIA CUDA GPUs to attain a level of performance equivalent to hundreds of processors on a fast cluster.
GROMA High performance
Y Y Y Free gromacs.org
CS MD 17 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
GROMO Geared towards GROMOS Y Y Y Y Y Y Not free
S biomolecules Homepage
Molecular dynamics Free for https://projects.iv GULP Y Y and Lattice academic
ec.org/gulp/ optimization use
General-purpose Molecular Dynamics highly optimized for GPUs. Includes various pair Free, http://codeblue.u HOOMD Y Y Y potentials, Brownian open mich.edu/hoomd- -blue
dynamics, source blue/index.html dissipative particle dynamics, rigid body constraints, energy minimization, etc...
Powerful global optimizer in an arbitrary subset of internal variables,
ICM Y Y Y Y I Y NOEs, Protein Not free Molsoft
docking, Ligand docking, Peptide docking, EM, Density placement
Has potentials for soft and solid-state LAMMP
Y Y Y Y I Y materials and Free Sandia
S coarse-grain systems
OPLS-AA, MMFF, GBSA solvent model, conformational sampling, MacroM Commerci
Y Y Y Y Y I Y minimization, MD. Schrödinger odel al Includes the Maestro GUI which provides visualization, molecule building,
18 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
calculation setup, job launching and monitoring, project- level organization of results and access to a suite of other modelling programs.
Building, visualization and Closed analysis tools in a source/Tr
MAPS Y Y Y Y Y Y Y single user interface Scienomics ial together with access available to multiple simulation engines.
Materials Studio is a software environment that brings the materials Closed Material simulation source/Tr
Y Y Y Y Y Y Y Y Accelrys s Studio technology to ial desktop computing, available solving key problems throughout the R&D process.
MedeA combines leading experimental databases and major computational programs like the Closed Vienna Ab-Initio source/Tr
MedeA Y Y Y Y Y Y Simulation Package Materials Design ial (VASP), LAMMPS, available GIBBS with sophisticated materials property prediction, analysis, and visualization.
Originally designed MCCCS
Y for the prediction of Free Towhee Project
Towhee fluid phase 19 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
equilibria
MDyna Stockholm Y Parallel MD Free
Mix University
Molecular Operating Commerci Chemical
MOE Y Y Y Y I Y
Environment al Computing Group
Also includes action- based algorithms (Stochastic Difference Equation in Time and
MOIL Y Y Y Y Free link Stochastic Difference Equation in Length) and locally enhanced sampling.
Simple Javascript molecoo
Y Y molecular link ls visualization tool
Parallel, only pair- potentials, Cell lists,
MOLDY Y Free Moldy modified Beeman's algorithm
A Molecular Dynamics Simulation Program Free, to Explore Free ORAC download
ORAC Y Y Y Y open
Energy Surfaces in page source Biomolecular Systems at the Atomistic Level
Generation of Models for [4] NAB Y Free Case group "Unusual" DNA and RNA
Builds complex Packmo initial configurations
Y link l for Molecular Dynamics
20 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
Mod View I G Nam el M RE Q Licens Min MD m P Comments Website e Buil C M M e p U 3D der
Homology modeling, loop and side chain optimization, Commerci
Prime Y Y Y Y I Y Schrödinger minimization, OPLS- al AA, SGB solvent model, parallalized
Protein Helix, loop, and side Local chain optimization.
Optimiz Y Y Y Y Not free PLOP wiki Fast energy ation minimization.
Program
Python-based viewer, structure builder and VASP results browser. Free,
p4vasp Y Y Shows band- open p4vasp.at
structure, charge source densities and simulates STM images.
Python-based viewer, many Free,
PyMOL Y Y plugins to other open PyMol.org
software. Some source mutagenisis.
Protein viewer,
QMOL Y provided Free DNASTAR, Inc.
by DNASTAR
RasMol Y Fast viewer Free RasMol
Raster3 High quality raster University of Y Free
D images Washington
Reduced MD. Free on RedMD[ University of I Y Y Y Y Package for coarse- GNU 5] Warsaw, ICM grained simulations. Licence
StruMM Sophisticated 3-D The 200 3D molecule builder atom
Y Y Y Y ' ' Exorga, Inc. (STR3DI and viewer, version is
32) advanced structural free
21 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
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analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking and the handling of complexes.
Selvita Protein structure Protein prediction, homology Modelin modeling, ab Commerci
Y Y Y Y Selvita Ltd g initio modeling, loop al Platfor modeling,protein
m threading
MM, DFT, Semiempi rical methods, parallelMD, conformational analysis, Linear scaling SCF, docking SCIGRE protein- Commerci
Y Y Y Y Y Y SCIGRESS.com
SS ligand, Batch al processing, Virtual screening, Automated builders (molecular dynamics, proteins, crystals)
SimBio Sys' molecular MoDeST docking, scoring (Molecul functions for ar Y Y Y Y Not Free SimBioSys Inc. docking, "ligand- Design based", "fragment- Softwar based", "de-novo" e
Toolkit)
Small molecule (< Commerci
Spartan Y Y Y Y Y Y Wavefunction, Inc. 2000 a.m.u.) MM al, Trial 22 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
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and QM tools for Available determining conformation, structure, property, spectra, reactivity, and selectivity.
Web server to determine automatically Free for parameters and academic. topologies for small CHARMm SwissPa organic molecules, licence
SwissParam. ram for use with the required CHARMM all atoms for force field. Files can commerci be used with al usage. CHARMM and GROMACS.
High performance GPU- accelerated ab initioMolecular Dynamics and TD/DFT software Closed package for very source / TeraChe large molecular or
Y Y Y Y Trial PetaChem LLC m evennanoscale syste licenses ms. The software available runs onNVIDIA GPUs and 64-bit Linux, and is based on heavily optimized CUDA cod e.
Software tools for Washington
TINKER I Y Y Y Y I Y Free
molecular design University
Tremolo
I Y Y Fast, parallel MD Not Free Tremolo-X
-X
UCSF Y Y Y Visually appealing University of
23 Blog Journal: A journal which focus on short and straight articles which publishes the articles in respective field or area, also presented online by blogging.
Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
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Chimer viewer, amino acid California
a rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development.
3D viewer, multiple file format support, 2D and 3D editor, surface calculation, conformational analysis, MOPAC an Free for VEGA d NAMDinterfaces,
Y Y Y I Y Y Y academic VEGA ZZ Web site
ZZ MD trajectory use analysis, molecular docking, virtual screening, database engine, parallel design, OpenCL acce leration, etc.
Complete Molecular Modelling Software, QSAR, VLifeM Combinetorial Vlife Sciences Y Y Y Y I Y Not free
DS Library generation, Technologies Pharmacophore, Cheminformatics, docking, etc.
Open source, VMD + Fast, parallel MD,
Y Y Y Y Y Y Y free to Beckman Institute NAMD CUDA academic s
Visualizer for MD. WHAT
Y Y I I I Interface to Not free WHAT IF
IF GROMACS.
open project xeo Y Y link management for
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Open Access Chemistry-The Blog Journal Vol 1, Issue1, 13-26, 2013. Visit: www.openaccess-chemistry.com
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nanostructures
Molecular-graphics,
YASARA Y Y Y Y Y -modeling and - Not free YASARA.org
simulation program
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
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