Software:Discovery Studio
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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 Systèmes BIOVIA[1] (formerly Accelrys).
The product suite has a strong academic collaboration programme,[2] supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including CHARMM,[3] MODELLER,[4] DELPHI,[5] ZDOCK,[6] DMol3[7][8] 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[9][10]
- Structure-based Design
- Including tools for fragment-based placement and refinement,[11] receptor-ligand docking and pose refinement, de novo design
- Macromolecule design and validation
- Macromolecule engineering
- Specialist tools for protein-protein docking[12]
- Specialist tools for Antibody design[13] 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
References
- ↑ "BIOVIA". August 11, 2023. https://www.3ds.com/products/biovia.
- ↑ "List of key Accelrys academic collaborators". Archived from the original on November 25, 2011. https://web.archive.org/web/20111125063145/http://accelrys.com/innovation/academic-collaborator-program/.
- ↑ Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G. et al. (2009-07-30). "CHARMM: The biomolecular simulation program". Journal of Computational Chemistry 30 (10): 1545–1614. doi:10.1002/jcc.21287. ISSN 0192-8651. PMID 19444816. PMC 2810661. http://deepblue.lib.umich.edu/bitstream/2027.42/63074/1/21287_ftp.pdf.
- ↑ Webb, Benjamin; Sali, Andrej (2016). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics 54 (1): Supplement 15, 5.6.1-5.6.30. doi:10.1002/cpbi.3. ISSN 1934-3396. PMID 27322406.
- ↑ Rocchia, W.; Alexov, E.; Honig, B. (2001-07-01). "Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions". The Journal of Physical Chemistry B 105 (28): 6507–6514. doi:10.1021/jp010454y. ISSN 1520-6106. https://pubs.acs.org/doi/10.1021/jp010454y.
- ↑ Chen, Rong; Li, Li; Weng, Zhiping (2003). "ZDOCK: An initial-stage protein-docking algorithm". Proteins: Structure, Function, and Bioinformatics 52 (1): 80–87. doi:10.1002/prot.10389. ISSN 0887-3585. PMID 12784371. https://onlinelibrary.wiley.com/doi/10.1002/prot.10389.
- ↑ Matsuzawa, Nobuyuki; Seto, Jun'etsu; Dixon, David A. (1997-12-01). "Density Functional Theory Predictions of Second-Order Hyperpolarizabilities of Metallocenes". The Journal of Physical Chemistry A 101 (49): 9391–9398. doi:10.1021/jp952465v. ISSN 1089-5639. Bibcode: 1997JPCA..101.9391M. https://pubs.acs.org/doi/10.1021/jp952465v.
- ↑
- Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules". The Journal of Chemical Physics (AIP Publishing) 92 (1): 508–517. doi:10.1063/1.458452. ISSN 0021-9606. Bibcode: 1990JChPh..92..508D. https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58936/datastream/PDF/Delley-1990-An_all-electron_numerical_method_for-%28published_version%29.pdf.
- Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach". The Journal of Chemical Physics (AIP Publishing) 94 (11): 7245–7250. doi:10.1063/1.460208. ISSN 0021-9606. Bibcode: 1991JChPh..94.7245D. https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58947/datastream/PDF/Delley-1991-Analytic_energy_derivatives_in_the-%28published_version%29.pdf.
- Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach". The Journal of Chemical Physics (AIP Publishing) 113 (18): 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606. https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A58939/datastream/PDF/Delley-2000-From_molecules_to_solids_with-%28published_version%29.pdf.
- ↑ Sutter, Jon; Li, Jiabo; Maynard, Allister J.; Goupil, Anne; Luu, Tien; Nadassy, Katalin (2011). "New Features that Improve the Pharmacophore Tools from Accelrys". Current Computer-Aided Drug Design 7 (3): 173–180. doi:10.2174/157340911796504305. PMID 21726193. https://www.eurekaselect.com/article/18827.
- ↑ Luu, Tien T. T.; Malcolm, Noj; Nadassy, Katalin (2011). "Pharmacophore Modeling Methods in Focused Library Selection – Applications in the Context of a New Classification Scheme". Combinatorial Chemistry & High Throughput Screening 14 (6): 488–499. doi:10.2174/138620711795767820. PMID 21521148. https://www.eurekaselect.com/article/19211.
- ↑ Haider, Muhammad K.; Bertrand, Hugues-Olivier; Hubbard, Roderick E. (2011-05-23). "Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach". Journal of Chemical Information and Modeling 51 (5): 1092–1105. doi:10.1021/ci100469n. ISSN 1549-9596. PMID 21528911. https://pubs.acs.org/doi/10.1021/ci100469n.
- ↑ Corradi, Valentina; Mancini, Manuela; Santucci, Maria Alessandra; Carlomagno, Teresa; Sanfelice, Domenico; Mori, Mattia; Vignaroli, Giulia; Falchi, Federico et al. (2011). "Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case". Bioorganic & Medicinal Chemistry Letters (Elsevier BV) 21 (22): 6867–6871. doi:10.1016/j.bmcl.2011.09.011. ISSN 0960-894X. PMID 21962576.
- ↑ Almagro, Juan C.; Beavers, Mary Pat; Hernandez-Guzman, Francisco; Maier, Johannes; Shaulsky, Jodi; Butenhof, Kenneth; Labute, Paul; Thorsteinson, Nels et al. (2011). "Antibody modeling assessment". Proteins: Structure, Function, and Bioinformatics 79 (11): 3050–3066. doi:10.1002/prot.23130. ISSN 0887-3585. PMID 21935986. https://onlinelibrary.wiley.com/doi/10.1002/prot.23130.
External links
- Accelrys.com
- Discovery Studio
- Supporting free software tools: Discovery Studio Visualizer and ActiveX Controls
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