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Molecular Modelling Softwares-Open Sources Available for Drug Design & Discovery 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. 12 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 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. 14 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 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.
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