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Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA (formerly Accelrys).
The product suite has a strong academic collaboration programme, supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including CHARMM,[1] MODELLER,[2] DELPHI,[3] ZDOCK,[4] DMol3[5][6] and more.
Scope
Discovery Studio provides software applications covering the following areas:
Simulations
Including Molecular Mechanics, Molecular Dynamics, Quantum Mechanics
For molecular mechanics based simulations: Include implicit and explicit-based solvent models and membrane models
Also includes the ability to perform hybrid QM/MM calculations
Ligand Design
Including tools for enumerating molecular libraries and library optimization
Pharmacophore modeling
Including creation, validation and virtual screening[7][8]
Structure-based Design
Including tools for fragment-based placement and refinement,[9] receptor-ligand docking and pose refinement, de novo design
Macromolecule design and validation
Macromolecule engineering
Specialist tools for protein-protein docking[10]
Specialist tools for Antibody design[11] and optimization
Specialist tools for membrane-bound proteins, including GPCRs
QSAR
Covering methods such as multiple linear regression, partial least squares, recursive partitioning, Genetic Function approximation and 3D field-based QSAR
ADME
Predictive toxicity
See also
Molecular Mechanics Programs
Quantum Mechanics Software
Molecular Modeling
Molecular Design Software
Protein homology modeling
MDL Chime
External links
Accelrys.com
Discovery Studio
Supporting free software tools: Discovery Studio Visualizer and ActiveX Controls
Recent News Articles
BioIT World News article on Discovery Studio
BioInform (GenomeWeb)
References
Brooks B. R., Brooks III C. L., Mackerell A. D., Nilsson L., Petrella R. J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A. R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R. W., Post C. B., Pu J. Z., Schaefer M., Tidor B., Venable R. M., Woodcock H. L., Wu X., Yang W., York D. M. and Karplus M. CHARMM: The Biomolecular simulation Program, J. Comput. Chem. 2009, 30, 1545-1615.
Eswar N., Marti-Renom M.A., Webb B., Madhusudhan M.S., Eramian D., Shen M., Pieper U., Sali A. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., 2006, Supplement 15, 5.6.1-5.6.30.
W.Rocchia, E.Alexov, and B.Honig. Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions. J. Phys. Chem. B, 2001, 105, 6507-6514.
Chen R., Weng Z. ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins 2003, 52, 80-87.
Matsuzawa N., Seto J., DixonD. A., J. Phys. Chem. A, 1997, 101, 9391.
Delley Bi, J. Chem. Phys., 1990, 92, 508; ibid, 1991, 94, 7245; ibid, 2000, 7756.
Sutter A., Jiabo L., Maynard A.J., Goupil A., Luu T., Katalin N., New Features that Improve the Pharmacophore Tools from Accelrys
Luu T., Malcolm N., Nadassy K., Pharmacophore Modeling Methods in Focused Library Selection -Applications in the Context of a New Classification Scheme, Comb. Chem. & High Thr. Screening, 2011, 14(6), pp. 488-499(12)
Haider M.K., Bertrand H.-O., Hubbard R.E., Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach, J. Chem. Inf. Model., 2011, 51 (5), pp 1092–1105
Corradia V., Mancinib M, Santuccib M.A., Carlomagnoc T., Sanfelicec D., Moria M., Vignarolia G., Falchia F., Manettia F., Radia M., Botta M., Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case
Almagro J.C., Beavers M.P., Hernandez-Guzman F., Maier J., Shaulsky J., Butenhof K., Labute P., Thorsteinson N., Kelly K., Teplyakov A., Luo J., Sweet R., Gilliland G.L., Antibody modeling assessment, Proteins: Structure, Function, and Bioinformatics, 2011, 79(11), pages 3050–3066.
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Computational chemistry software
Cheminformatics
Free software
Avalon Cheminformatics Toolkit Bioclipse Blue Obelisk Chemistry Development Kit ECCE JOELib OELib Open Babel RDKit
Proprietary
Canvas Chemicalize Discovery Studio
Chemical kinetics
Free software
APBS Cantera KPP
Proprietary
Autochem Chemical WorkBench CHEMKIN COSILAB DelPhi Khimera
Molecular modelling
and
visualization
List of molecular graphics systems
Free software
Ascalaph Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol
Proprietary
Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow EzMol Gaussian Maestro MarvinSketch MarvinView MODELLER Molecular Operating Environment SAMSON Spartan UCSF Chimera VMD
Molecular docking
List of protein-ligand docking software
Free software
AutoDock AutoDock Vina FlexAID rDock
Proprietary
Glide LeDock Molecular Operating Environment
Molecular dynamics
Free software
CP2K GROMACS LAMMPS OpenMM PLUMED
Proprietary
Abalone AMBER CHARMM CPMD Desmond GROMOS NAMD
Quantum chemistry
List of quantum chemistry and solid-state physics software
Free software
ABINIT ACES (CFOUR) AIMAll BigDFT COLUMBUS CONQUEST CP2K Dalton DIRAC DP code FLEUR FreeON MADNESS MPQC NWChem Octopus OpenMolcas PARSEC PSI PyQuante PySCF Quantum ESPRESSO (PWscf) RMG SIESTA VB2000 YAMBO code
Proprietary
ADF AMPAC DMol3 CADPAC CASINO CASTEP CPMD CRUNCH CRYSTAL Firefly GAMESS (UK) GAMESS (US) Gaussian Jaguar MOLCAS MOLPRO MOPAC ONETEP OpenAtom ORCA PLATO PQS Q-Chem Quantemol Scigress Spartan TeraChem TURBOMOLE VASP WIEN2k XMVB
Skeletal structure drawing
Free software
JChemPaint Molsketch XDrawChem
Proprietary
ACD/ChemSketch BIOVIA Draw ChemDoodle ChemDraw ChemWindow JME Molecule Editor MarvinSketch
Others
Aqion Eulim EXC code GenX GSim Mercury CrystalExplorer ICM (ICM-Browser) Materials Studio Molden OpenChrom SASHIMI
Hellenica World - Scientific Library
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