请输入您要查询的百科知识:

 

词条 Discovery Studio
释义

  1. Scope

  2. See also

  3. External links

  4. Recent News Articles

  5. References

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by 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

1. ^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.
2. ^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.
3. ^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.
4. ^Chen R., Weng Z. ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins 2003, 52, 80-87.
5. ^Matsuzawa N., Seto J., DixonD. A., J. Phys. Chem. A, 1997, 101, 9391.
6. ^Delley Bi, J. Chem. Phys., 1990, 92, 508; ibid, 1991, 94, 7245; ibid, 2000, 7756.
7. ^Sutter A., Jiabo L., Maynard A.J., Goupil A., Luu T., Katalin N., New Features that Improve the Pharmacophore Tools from Accelrys
8. ^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)
9. ^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
10. ^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
11. ^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.

{{Chemistry software}}

2 : Computational chemistry software|Science software

随便看

 

开放百科全书收录14589846条英语、德语、日语等多语种百科知识,基本涵盖了大多数领域的百科知识,是一部内容自由、开放的电子版国际百科全书。

 

Copyright © 2023 OENC.NET All Rights Reserved
京ICP备2021023879号 更新时间:2024/9/20 16:52:32