Discovery Studio

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

References

^ "BIOVIA". Dassault Systèmes. August 11, 2023.
^ "List of key Accelrys academic collaborators". accelrys.com. Archived from the original on November 25, 2011.
^ Brooks, B. R.; Brooks, 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.; Karplus, M. (2009-07-30). "CHARMM: The biomolecular simulation program" (PDF). Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. ISSN 0192-8651. PMC 2810661. PMID 19444816.
^ 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. PMC 5031415. 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.
^ 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.
^ 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. Bibcode:1997JPCA..101.9391M. doi:10.1021/jp952465v. ISSN 1089-5639.
^
- Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.
- Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.
- Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.
^ 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.
^ 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.
^ 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.
^ Corradi, Valentina; Mancini, Manuela; Santucci, Maria Alessandra; Carlomagno, Teresa; Sanfelice, Domenico; Mori, Mattia; Vignaroli, Giulia; Falchi, Federico; Manetti, Fabrizio; Radi, Marco; Botta, Maurizio (2011). "Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case". Bioorganic & Medicinal Chemistry Letters. 21 (22). Elsevier BV: 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; Kelly, Kenneth; Teplyakov, Alexey; Luo, Jinquan; Sweet, Raymond; Gilliland, Gary L. (2011). "Antibody modeling assessment". Proteins: Structure, Function, and Bioinformatics. 79 (11): 3050–3066. doi:10.1002/prot.23130. ISSN 0887-3585. PMID 21935986.

External links

Accelrys.com
Discovery Studio
Supporting free software tools: Discovery Studio Visualizer and ActiveX Controls Archived 2011-11-19 at the Wayback Machine

Recent News Articles

BioIT World News article on Discovery Studio Archived 2011-10-07 at the Wayback Machine
BioInform (GenomeWeb)

[1] "BIOVIA". Dassault Systèmes. August 11, 2023.

[2] "List of key Accelrys academic collaborators". accelrys.com. Archived from the original on November 25, 2011.

[3] Brooks, B. R.; Brooks, 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.; Karplus, M. (2009-07-30). "CHARMM: The biomolecular simulation program" (PDF). Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. ISSN 0192-8651. PMC 2810661. PMID 19444816.

[4] 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. PMC 5031415. PMID 27322406.

[5] 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.

[6] 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.

[7] 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. Bibcode:1997JPCA..101.9391M. doi:10.1021/jp952465v. ISSN 1089-5639.

[8] 
Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.
Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.
Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.

[9] Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.

[10] Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.

[11] Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.

[9] 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.

[10] 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.

[11] 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.

[12] Corradi, Valentina; Mancini, Manuela; Santucci, Maria Alessandra; Carlomagno, Teresa; Sanfelice, Domenico; Mori, Mattia; Vignaroli, Giulia; Falchi, Federico; Manetti, Fabrizio; Radi, Marco; Botta, Maurizio (2011). "Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case". Bioorganic & Medicinal Chemistry Letters. 21 (22). Elsevier BV: 6867–6871. doi:10.1016/j.bmcl.2011.09.011. ISSN 0960-894X. PMID 21962576.

[13] Almagro, Juan C.; Beavers, Mary Pat; Hernandez-Guzman, Francisco; Maier, Johannes; Shaulsky, Jodi; Butenhof, Kenneth; Labute, Paul; Thorsteinson, Nels; Kelly, Kenneth; Teplyakov, Alexey; Luo, Jinquan; Sweet, Raymond; Gilliland, Gary L. (2011). "Antibody modeling assessment". Proteins: Structure, Function, and Bioinformatics. 79 (11): 3050–3066. doi:10.1002/prot.23130. ISSN 0887-3585. PMID 21935986.

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Scope

See also

References

External links

Recent News Articles