Discovery Studio

{{Prose|date=May 2024}}

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA{{Cite web|url=https://www.3ds.com/products/biovia|title=BIOVIA|date=August 11, 2023|website=Dassault Systèmes}} (formerly Accelrys).

The product suite has a strong academic collaboration programme,{{Cite web|url=http://accelrys.com/innovation/academic-collaborator-program/|archiveurl=https://web.archive.org/web/20111125063145/http://accelrys.com/innovation/academic-collaborator-program/|url-status=dead|title=List of key Accelrys academic collaborators|archivedate=November 25, 2011|website=accelrys.com}} supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including CHARMM,{{cite journal | last1=Brooks | first1=B. R. | last2=Brooks | first2=C. L. | last3=Mackerell | first3=A. D. | last4=Nilsson | first4=L. | last5=Petrella | first5=R. J. | last6=Roux | first6=B. | last7=Won | first7=Y. | last8=Archontis | first8=G. | last9=Bartels | first9=C. | last10=Boresch | first10=S. | last11=Caflisch | first11=A. | last12=Caves | first12=L. | last13=Cui | first13=Q. | last14=Dinner | first14=A. R. | last15=Feig | first15=M. | last16=Fischer | first16=S. | last17=Gao | first17=J. | last18=Hodoscek | first18=M. | last19=Im | first19=W. | last20=Kuczera | first20=K. | last21=Lazaridis | first21=T. | last22=Ma | first22=J. | last23=Ovchinnikov | first23=V. | last24=Paci | first24=E. | last25=Pastor | first25=R. W. | last26=Post | first26=C. B. | last27=Pu | first27=J. Z. | last28=Schaefer | first28=M. | last29=Tidor | first29=B. | last30=Venable | first30=R. M. | last31=Woodcock | first31=H. L. | last32=Wu | first32=X. | last33=Yang | first33=W. | last34=York | first34=D. M. | last35=Karplus | first35=M. | title=CHARMM: The biomolecular simulation program | journal=Journal of Computational Chemistry | volume=30 | issue=10 | date=2009-07-30 | issn=0192-8651 | pmid=19444816 | pmc=2810661 | doi=10.1002/jcc.21287 | doi-access=free | pages=1545–1614 | url=http://deepblue.lib.umich.edu/bitstream/2027.42/63074/1/21287_ftp.pdf }} MODELLER,{{cite journal | last1=Webb | first1=Benjamin | last2=Sali | first2=Andrej | title=Comparative Protein Structure Modeling Using MODELLER | journal=Current Protocols in Bioinformatics | volume=54 | issue=1 | date=2016 | issn=1934-3396 | pmid=27322406 | pmc=5031415 | doi=10.1002/cpbi.3 | doi-access=free |at= Supplement 15, 5.6.1-5.6.30}} DELPHI,{{cite journal | last1=Rocchia | first1=W. | last2=Alexov | first2=E. | last3=Honig | first3=B. | title=Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions | journal=The Journal of Physical Chemistry B | volume=105 | issue=28 | date=2001-07-01 | issn=1520-6106 | doi=10.1021/jp010454y | pages=6507–6514 | url=https://pubs.acs.org/doi/10.1021/jp010454y | url-access=subscription }} ZDOCK,{{cite journal | last1=Chen | first1=Rong | last2=Li | first2=Li | last3=Weng | first3=Zhiping | title=ZDOCK: An initial-stage protein-docking algorithm | journal=Proteins: Structure, Function, and Bioinformatics | volume=52 | issue=1 | date=2003 | issn=0887-3585 | doi=10.1002/prot.10389 | pages=80–87 | pmid=12784371 | url=https://onlinelibrary.wiley.com/doi/10.1002/prot.10389 | url-access=subscription }} DMol3{{cite journal | last1=Matsuzawa | first1=Nobuyuki | last2=Seto | first2=Jun'etsu | last3=Dixon | first3=David A. | title=Density Functional Theory Predictions of Second-Order Hyperpolarizabilities of Metallocenes | journal=The Journal of Physical Chemistry A | volume=101 | issue=49 | date=1997-12-01 | issn=1089-5639 | doi=10.1021/jp952465v | pages=9391–9398 | bibcode=1997JPCA..101.9391M | url=https://pubs.acs.org/doi/10.1021/jp952465v | url-access=subscription }}{{multiref2|{{cite journal | last=Delley | first=B. | title=An all-electron numerical method for solving the local density functional for polyatomic molecules | journal=The Journal of Chemical Physics | publisher=AIP Publishing | volume=92 | issue=1 | date=1990-01-01 | issn=0021-9606 | doi=10.1063/1.458452 | doi-access=free | pages=508–517 | bibcode=1990JChPh..92..508D | url=https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58936/datastream/PDF/Delley-1990-An_all-electron_numerical_method_for-%28published_version%29.pdf }}| {{cite journal | last=Delley | first=B. | title=Analytic energy derivatives in the numerical local-density-functional approach | journal=The Journal of Chemical Physics | publisher=AIP Publishing | volume=94 | issue=11 | date=1991-06-01 | issn=0021-9606 | doi=10.1063/1.460208 | doi-access=free | pages=7245–7250 | bibcode=1991JChPh..94.7245D | url=https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58947/datastream/PDF/Delley-1991-Analytic_energy_derivatives_in_the-%28published_version%29.pdf }}| {{cite journal | last=Delley | first=B. | title=From molecules to solids with the DMol3 approach | journal=The Journal of Chemical Physics | publisher=AIP Publishing | volume=113 | issue=18 | date=2000-11-08 | issn=0021-9606 | doi=10.1063/1.1316015 | doi-access=free | pages=7756–7764 | url=https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58939/datastream/PDF/Delley-2000-From_molecules_to_solids_with-%28published_version%29.pdf }}}} 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{{cite journal | last1=Sutter | first1=Jon | last2=Li | first2=Jiabo | last3=Maynard | first3=Allister J. | last4=Goupil | first4=Anne | last5=Luu | first5=Tien | last6=Nadassy | first6=Katalin | title=New Features that Improve the Pharmacophore Tools from Accelrys | journal=Current Computer-Aided Drug Design | date=2011 | volume=7 | issue=3 | doi=10.2174/157340911796504305 | pages=173–180 | pmid=21726193 | url=https://www.eurekaselect.com/article/18827 | url-access=subscription }}{{cite journal | last1=Luu | first1=Tien T. T. | last2=Malcolm | first2=Noj | last3=Nadassy | first3=Katalin | title=Pharmacophore Modeling Methods in Focused Library Selection – Applications in the Context of a New Classification Scheme | journal=Combinatorial Chemistry & High Throughput Screening | date=2011 | volume=14 | issue=6 | doi=10.2174/138620711795767820 | pages=488–499 | pmid=21521148 | url=https://www.eurekaselect.com/article/19211 | url-access=subscription }}
  • Structure-based Design
  • Including tools for fragment-based placement and refinement,{{cite journal | last1=Haider | first1=Muhammad K. | last2=Bertrand | first2=Hugues-Olivier | last3=Hubbard | first3=Roderick E. | title=Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach | journal=Journal of Chemical Information and Modeling | volume=51 | issue=5 | date=2011-05-23 | issn=1549-9596 | doi=10.1021/ci100469n | pages=1092–1105 | pmid=21528911 | url=https://pubs.acs.org/doi/10.1021/ci100469n | url-access=subscription }} receptor-ligand docking and pose refinement, de novo design
  • Macromolecule design and validation
  • Macromolecule engineering
  • Specialist tools for protein-protein docking{{cite journal | last1=Corradi | first1=Valentina | last2=Mancini | first2=Manuela | last3=Santucci | first3=Maria Alessandra | last4=Carlomagno | first4=Teresa | last5=Sanfelice | first5=Domenico | last6=Mori | first6=Mattia | last7=Vignaroli | first7=Giulia | last8=Falchi | first8=Federico | last9=Manetti | first9=Fabrizio | last10=Radi | first10=Marco | last11=Botta | first11=Maurizio | title=Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case | journal=Bioorganic & Medicinal Chemistry Letters | publisher=Elsevier BV | volume=21 | issue=22 | year=2011 | issn=0960-894X | doi=10.1016/j.bmcl.2011.09.011 | pages=6867–6871| pmid=21962576 }}
  • Specialist tools for Antibody design{{cite journal | last1=Almagro | first1=Juan C. | last2=Beavers | first2=Mary Pat | last3=Hernandez-Guzman | first3=Francisco | last4=Maier | first4=Johannes | last5=Shaulsky | first5=Jodi | last6=Butenhof | first6=Kenneth | last7=Labute | first7=Paul | last8=Thorsteinson | first8=Nels | last9=Kelly | first9=Kenneth | last10=Teplyakov | first10=Alexey | last11=Luo | first11=Jinquan | last12=Sweet | first12=Raymond | last13=Gilliland | first13=Gary L. | title=Antibody modeling assessment | journal=Proteins: Structure, Function, and Bioinformatics | volume=79 | issue=11 | date=2011 | issn=0887-3585 | doi=10.1002/prot.23130 | pages=3050–3066 | pmid=21935986 | url=https://onlinelibrary.wiley.com/doi/10.1002/prot.23130 | url-access=subscription }} 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

References

{{reflist}}

=Recent News Articles=

  • [http://www.bio-itworld.com/news/07/13/11/Updated-Accelrys-discovery-studio-targets-protein-aggregation.html BioIT World News article on Discovery Studio] {{Webarchive|url=https://web.archive.org/web/20111007050234/http://www.bio-itworld.com/news/07/13/11/Updated-Accelrys-discovery-studio-targets-protein-aggregation.html |date=2011-10-07 }}
  • [http://www.genomeweb.com/informatics/accelrys-adds-protein-aggregation-prediction-algorithm-latest-discovery-studio-r BioInform (GenomeWeb)]

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